I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 23 06:11:27 -12 2020 I: pbuilder-time-stamp: 1600884687 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gromacs_2019.1-1.dsc] I: copying [./gromacs_2019.1.orig.tar.gz] I: copying [./gromacs_2019.1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Feb 17 06:12:37 2019 -12 gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F gpgv: issuer "nbreen@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gromacs_2019.1-1.dsc dpkg-source: info: extracting gromacs in gromacs-2019.1 dpkg-source: info: unpacking gromacs_2019.1.orig.tar.gz dpkg-source: info: unpacking gromacs_2019.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying doxygen.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying local-mathjax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/13803/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='794237dbc32441e0b26b27ac65df8472' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='13803' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.ckfjStxYZY/pbuilderrc_rnxT --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ckfjStxYZY/b1 --logfile b1/build.log gromacs_2019.1-1.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux jtx1a 4.19.0-10-arm64 #1 SMP Debian 4.19.132-1 (2020-07-24) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 20 20:27 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/13803/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: chrpath, cmake, debhelper (>= 11), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, mpich, openmpi-bin, zlib1g-dev, doxygen, ghostscript, graphviz, imagemagick, mscgen, python-sphinx (>= 1.4.1), rdfind, symlinks, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper (>= 11); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libmpich-dev (>= 3.0.4-6); however: Package libmpich-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev (>= 1.10.2-7); however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libx11-dev; however: Package libx11-dev is not installed. pbuilder-satisfydepends-dummy depends on mpich; however: Package mpich is not installed. pbuilder-satisfydepends-dummy depends on openmpi-bin; however: Package openmpi-bin is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on mscgen; however: Package mscgen is not installed. pbuilder-satisfydepends-dummy depends on python-sphinx (>= 1.4.1); however: Package python-sphinx is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. pbuilder-satisfydepends-dummy depends on symlinks; however: Package symlinks is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lmodern{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} ghostscript{a} graphviz{a} groff-base{a} hicolor-icon-theme{a} hwloc-nox{a} ibverbs-providers{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.67-dev{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libclang1-6.0{a} libcroco3{a} libcups2{a} libcupsimage2{a} libcurl4{a} libdatrie1{a} libdbus-1-3{a} libde265-0{a} libedit2{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libexpat1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgd3{a} libgfortran-8-dev{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgs9{a} libgs9-common{a} libgssapi-krb5-2{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz-icu0{a} libharfbuzz0b{a} libheif1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu63{a} libidn11{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} libllvm6.0{a} liblqr-1-0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmagickcore-6.q16-6{a} libmagickwand-6.q16-6{a} libmpich-dev{a} libmpich12{a} libncurses6{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libopenjp2-7{a} libopenmpi-dev{a} libopenmpi3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpciaccess0{a} libpipeline1{a} libpixman-1-0{a} libpmix2{a} libpng16-16{a} libpotrace0{a} libprocps7{a} libpsl5{a} libptexenc1{a} libpthread-stubs0-dev{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libssh2-1{a} libssl1.1{a} libsynctex2{a} libteckit0{a} libtexlua52{a} libtexlua53{a} libtexluajit2{a} libthai-data{a} libthai0{a} libtiff5{a} libtool{a} libuchardet0{a} libuv1{a} libwebp6{a} libwebpmux3{a} libwoff1{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx265-165{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxdot4{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libxxhash0{a} libzzip-0-13{a} lsb-base{a} m4{a} man-db{a} mime-support{a} mpich{a} mscgen{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} python{a} python-alabaster{a} python-babel{a} python-babel-localedata{a} python-certifi{a} python-chardet{a} python-docutils{a} python-idna{a} python-imagesize{a} python-jinja2{a} python-markupsafe{a} python-minimal{a} python-packaging{a} python-pkg-resources{a} python-pygments{a} python-pyparsing{a} python-requests{a} python-roman{a} python-six{a} python-sphinx{a} python-typing{a} python-tz{a} python-urllib3{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} symlinks{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} ucf{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xdg-utils{a} xml-core{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus docutils-doc fonts-droid-fallback fonts-liberation gsfonts javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libcupsfilters1 libfile-mimeinfo-perl libglib2.0-data libgpm2 libgts-bin libmagickcore-6.q16-6-extra libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lmodern lynx netpbm psmisc publicsuffix python-cryptography python-enum34 python-ipaddress python-openssl python-pil ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xauth xdg-user-dirs 0 packages upgraded, 262 newly installed, 0 to remove and 0 not upgraded. Need to get 197 MB of archives. After unpacking 765 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB] Get: 9 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libfftw3-double3 armhf 3.3.8-2 [432 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libpng16-16 armhf 1.6.36-6 [275 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libfreetype6 armhf 2.9.1-3+deb10u1 [322 kB] Get: 25 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 26 http://deb.debian.org/debian buster/main armhf ucf all 3.0038+nmu1 [69.0 kB] Get: 27 http://deb.debian.org/debian buster/main armhf fonts-dejavu-core all 2.37-1 [1068 kB] Get: 28 http://deb.debian.org/debian buster/main armhf fontconfig-config all 2.13.1-2 [280 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libfontconfig1 armhf 2.13.1-2 [328 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libde265-0 armhf 1.0.3-1+b1 [192 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libx265-165 armhf 2.9-4 [536 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libheif1 armhf 1.3.2-2~deb10u1 [107 kB] Get: 33 http://deb.debian.org/debian buster/main armhf libjbig0 armhf 2.1-3.1+b2 [28.4 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [112 kB] Get: 35 http://deb.debian.org/debian buster/main armhf liblcms2-2 armhf 2.9-3 [119 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 37 http://deb.debian.org/debian buster/main armhf liblqr-1-0 armhf 0.4.2-2.1 [23.5 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libltdl7 armhf 2.4.6-9 [387 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libopenjp2-7 armhf 2.3.0-2+deb10u1 [143 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libwebp6 armhf 0.6.1-2 [229 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libtiff5 armhf 4.1.0+git191117-2~deb10u1 [252 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libwebpmux3 armhf 0.6.1-2 [94.1 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libxcb1 armhf 1.13.1-2 [132 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libx11-data all 2:1.6.7-1 [298 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libx11-6 armhf 2:1.6.7-1 [698 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libxext6 armhf 2:1.3.3-1+b2 [48.1 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 51 http://deb.debian.org/debian buster/main armhf imagemagick-6-common all 8:6.9.10.23+dfsg-2.1+deb10u1 [200 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libmagickcore-6.q16-6 armhf 8:6.9.10.23+dfsg-2.1+deb10u1 [1644 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libmagickwand-6.q16-6 armhf 8:6.9.10.23+dfsg-2.1+deb10u1 [434 kB] Get: 54 http://deb.debian.org/debian buster/main armhf poppler-data all 0.4.9-2 [1473 kB] Get: 55 http://deb.debian.org/debian buster/main armhf sgml-base all 1.29 [14.8 kB] Get: 56 http://deb.debian.org/debian buster/main armhf tex-common all 6.11 [53.1 kB] Get: 57 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libprocps7 armhf 2:3.3.15-2 [58.7 kB] Get: 59 http://deb.debian.org/debian buster/main armhf lsb-base all 10.2019051400 [28.4 kB] Get: 60 http://deb.debian.org/debian buster/main armhf procps armhf 2:3.3.15-2 [248 kB] Get: 61 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 62 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 63 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 64 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libedit2 armhf 3.1-20181209-1 [79.5 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 71 http://deb.debian.org/debian buster/main armhf openssh-client armhf 1:7.9p1-10+deb10u2 [704 kB] Get: 72 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 73 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 74 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 75 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 76 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 77 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 78 http://deb.debian.org/debian buster/main armhf openssl armhf 1.1.1d-0+deb10u3 [818 kB] Get: 79 http://deb.debian.org/debian buster/main armhf ca-certificates all 20190110 [157 kB] Get: 80 http://deb.debian.org/debian buster/main armhf chrpath armhf 0.16-2+b1 [15.9 kB] Get: 81 http://deb.debian.org/debian buster/main armhf cmake-data all 3.13.4-1 [1476 kB] Get: 82 http://deb.debian.org/debian buster/main armhf libarchive13 armhf 3.3.3-4+deb10u1 [277 kB] Get: 83 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 84 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 85 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 86 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u2 [202 kB] Get: 87 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB] Get: 88 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get: 89 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get: 90 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB] Get: 91 http://deb.debian.org/debian buster/main armhf libcurl4 armhf 7.64.0-4+deb10u1 [297 kB] Get: 92 http://deb.debian.org/debian buster/main armhf libjsoncpp1 armhf 1.7.4-3 [67.8 kB] Get: 93 http://deb.debian.org/debian buster/main armhf librhash0 armhf 1.3.8-1 [134 kB] Get: 94 http://deb.debian.org/debian buster/main armhf libuv1 armhf 1.24.1-1 [98.0 kB] Get: 95 http://deb.debian.org/debian buster/main armhf cmake armhf 3.13.4-1 [2848 kB] Get: 96 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 97 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 98 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 99 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 100 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 101 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 102 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 103 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 104 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 105 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 106 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 107 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 108 http://deb.debian.org/debian buster/main armhf xml-core all 0.18+nmu1 [23.8 kB] Get: 109 http://deb.debian.org/debian buster/main armhf docutils-common all 0.14+dfsg-4 [167 kB] Get: 110 http://deb.debian.org/debian buster/main armhf libllvm6.0 armhf 1:6.0.1-10 [13.1 MB] Get: 111 http://deb.debian.org/debian buster/main armhf libclang1-6.0 armhf 1:6.0.1-10 [6029 kB] Get: 112 http://deb.debian.org/debian buster/main armhf doxygen armhf 1.8.13-10 [3568 kB] Get: 113 http://deb.debian.org/debian buster/main armhf fontconfig armhf 2.13.1-2 [404 kB] Get: 114 http://deb.debian.org/debian buster/main armhf fonts-lmodern all 2.004.5-6 [4539 kB] Get: 115 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 116 http://deb.debian.org/debian buster/main armhf libgfortran-8-dev armhf 8.3.0-6 [260 kB] Get: 117 http://deb.debian.org/debian buster/main armhf gfortran-8 armhf 8.3.0-6 [7219 kB] Get: 118 http://deb.debian.org/debian buster/main armhf gfortran armhf 4:8.3.0-1 [1424 B] Get: 119 http://deb.debian.org/debian buster/main armhf libgs9-common all 9.27~dfsg-2+deb10u3 [5136 kB] Get: 120 http://deb.debian.org/debian buster/main armhf libavahi-common-data armhf 0.7-4+b1 [122 kB] Get: 121 http://deb.debian.org/debian buster/main armhf libavahi-common3 armhf 0.7-4+b1 [51.1 kB] Get: 122 http://deb.debian.org/debian buster/main armhf libdbus-1-3 armhf 1.12.20-0+deb10u1 [191 kB] Get: 123 http://deb.debian.org/debian buster/main armhf libavahi-client3 armhf 0.7-4+b1 [54.5 kB] Get: 124 http://deb.debian.org/debian buster/main armhf libcups2 armhf 2.2.10-6+deb10u3 [291 kB] Get: 125 http://deb.debian.org/debian buster/main armhf libcupsimage2 armhf 2.2.10-6+deb10u3 [130 kB] Get: 126 http://deb.debian.org/debian buster/main armhf libidn11 armhf 1.33-2.2 [113 kB] Get: 127 http://deb.debian.org/debian buster/main armhf libijs-0.35 armhf 0.35-14 [16.7 kB] Get: 128 http://deb.debian.org/debian buster/main armhf libjbig2dec0 armhf 0.16-1 [54.5 kB] Get: 129 http://deb.debian.org/debian buster/main armhf libpaper1 armhf 1.1.28 [20.5 kB] Get: 130 http://deb.debian.org/debian buster/main armhf libgs9 armhf 9.27~dfsg-2+deb10u3 [1900 kB] Get: 131 http://deb.debian.org/debian buster/main armhf ghostscript armhf 9.27~dfsg-2+deb10u3 [94.5 kB] Get: 132 http://deb.debian.org/debian buster/main armhf libpixman-1-0 armhf 0.36.0-1 [465 kB] Get: 133 http://deb.debian.org/debian buster/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB] Get: 134 http://deb.debian.org/debian buster/main armhf libxcb-shm0 armhf 1.13.1-2 [99.0 kB] Get: 135 http://deb.debian.org/debian buster/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB] Get: 136 http://deb.debian.org/debian buster/main armhf libcairo2 armhf 1.16.0-4 [616 kB] Get: 137 http://deb.debian.org/debian buster/main armhf libcdt5 armhf 2.40.1-6 [58.1 kB] Get: 138 http://deb.debian.org/debian buster/main armhf libcgraph6 armhf 2.40.1-6 [77.3 kB] Get: 139 http://deb.debian.org/debian buster/main armhf libxpm4 armhf 1:3.5.12-1 [44.0 kB] Get: 140 http://deb.debian.org/debian buster/main armhf libgd3 armhf 2.2.5-5.2 [117 kB] Get: 141 http://deb.debian.org/debian buster/main armhf libgts-0.7-5 armhf 0.7.6+darcs121130-4 [137 kB] Get: 142 http://deb.debian.org/debian buster/main armhf libfribidi0 armhf 1.0.5-3.1+deb10u1 [61.7 kB] Get: 143 http://deb.debian.org/debian buster/main armhf libthai-data all 0.1.28-2 [170 kB] Get: 144 http://deb.debian.org/debian buster/main armhf libdatrie1 armhf 0.2.12-2 [35.8 kB] Get: 145 http://deb.debian.org/debian buster/main armhf libthai0 armhf 0.1.28-2 [50.7 kB] Get: 146 http://deb.debian.org/debian buster/main armhf libpango-1.0-0 armhf 1.42.4-8~deb10u1 [169 kB] Get: 147 http://deb.debian.org/debian buster/main armhf libgraphite2-3 armhf 1.3.13-7 [70.3 kB] Get: 148 http://deb.debian.org/debian buster/main armhf libharfbuzz0b armhf 2.3.1-1 [1151 kB] Get: 149 http://deb.debian.org/debian buster/main armhf libpangoft2-1.0-0 armhf 1.42.4-8~deb10u1 [62.7 kB] Get: 150 http://deb.debian.org/debian buster/main armhf libpangocairo-1.0-0 armhf 1.42.4-8~deb10u1 [52.2 kB] Get: 151 http://deb.debian.org/debian buster/main armhf libpathplan4 armhf 2.40.1-6 [61.3 kB] Get: 152 http://deb.debian.org/debian buster/main armhf libxdot4 armhf 2.40.1-6 [55.4 kB] Get: 153 http://deb.debian.org/debian buster/main armhf libgvc6 armhf 2.40.1-6 [556 kB] Get: 154 http://deb.debian.org/debian buster/main armhf libgvpr2 armhf 2.40.1-6 [189 kB] Get: 155 http://deb.debian.org/debian buster/main armhf x11-common all 1:7.7+19 [251 kB] Get: 156 http://deb.debian.org/debian buster/main armhf libice6 armhf 2:1.0.9-2 [51.7 kB] Get: 157 http://deb.debian.org/debian buster/main armhf liblab-gamut1 armhf 2.40.1-6 [220 kB] Get: 158 http://deb.debian.org/debian buster/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB] Get: 159 http://deb.debian.org/debian buster/main armhf libxt6 armhf 1:1.1.5-1+b3 [159 kB] Get: 160 http://deb.debian.org/debian buster/main armhf libxmu6 armhf 2:1.1.2-2+b3 [52.7 kB] Get: 161 http://deb.debian.org/debian buster/main armhf libxaw7 armhf 2:1.0.13-1+b2 [167 kB] Get: 162 http://deb.debian.org/debian buster/main armhf graphviz armhf 2.40.1-6 [518 kB] Get: 163 http://deb.debian.org/debian buster/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 164 http://deb.debian.org/debian buster/main armhf libhwloc5 armhf 1.11.12-3 [87.6 kB] Get: 165 http://deb.debian.org/debian buster/main armhf hwloc-nox armhf 1.11.12-3 [149 kB] Get: 166 http://deb.debian.org/debian buster/main armhf libnl-3-200 armhf 3.4.0-1 [55.6 kB] Get: 167 http://deb.debian.org/debian buster/main armhf libnl-route-3-200 armhf 3.4.0-1 [136 kB] Get: 168 http://deb.debian.org/debian buster/main armhf libibverbs1 armhf 22.1-1 [44.1 kB] Get: 169 http://deb.debian.org/debian buster/main armhf ibverbs-providers armhf 22.1-1 [20.2 kB] Get: 170 http://deb.debian.org/debian buster/main armhf imagemagick-6.q16 armhf 8:6.9.10.23+dfsg-2.1+deb10u1 [580 kB] Get: 171 http://deb.debian.org/debian buster/main armhf imagemagick armhf 8:6.9.10.23+dfsg-2.1+deb10u1 [156 kB] Get: 172 http://deb.debian.org/debian buster/main armhf libblas3 armhf 3.8.0-2 [109 kB] Get: 173 http://deb.debian.org/debian buster/main armhf libblas-dev armhf 3.8.0-2 [117 kB] Get: 174 http://deb.debian.org/debian buster/main armhf libboost1.67-dev armhf 1.67.0-13+deb10u1 [8388 kB] Get: 175 http://deb.debian.org/debian buster/main armhf libboost-dev armhf 1.67.0.1 [3860 B] Get: 176 http://deb.debian.org/debian buster/main armhf libbrotli1 armhf 1.0.7-2 [259 kB] Get: 177 http://deb.debian.org/debian buster/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [159 kB] Get: 178 http://deb.debian.org/debian buster/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [118 kB] Get: 179 http://deb.debian.org/debian buster/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB] Get: 180 http://deb.debian.org/debian buster/main armhf libfftw3-single3 armhf 3.3.8-2 [715 kB] Get: 181 http://deb.debian.org/debian buster/main armhf libfftw3-bin armhf 3.3.8-2 [43.5 kB] Get: 182 http://deb.debian.org/debian buster/main armhf libfftw3-dev armhf 3.3.8-2 [1141 kB] Get: 183 http://deb.debian.org/debian buster/main armhf libharfbuzz-icu0 armhf 2.3.1-1 [833 kB] Get: 184 http://deb.debian.org/debian buster/main armhf libltdl-dev armhf 2.4.6-9 [160 kB] Get: 185 http://deb.debian.org/debian buster/main armhf libhwloc-dev armhf 1.11.12-3 [153 kB] Get: 186 http://deb.debian.org/debian buster/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB] Get: 187 http://deb.debian.org/debian buster/main armhf ocl-icd-libopencl1 armhf 2.2.12-2 [35.6 kB] Get: 188 http://deb.debian.org/debian buster/main armhf libhwloc-plugins armhf 1.11.12-3 [15.7 kB] Get: 189 http://deb.debian.org/debian buster/main armhf libnl-3-dev armhf 3.4.0-1 [96.9 kB] Get: 190 http://deb.debian.org/debian buster/main armhf libnl-route-3-dev armhf 3.4.0-1 [162 kB] Get: 191 http://deb.debian.org/debian buster/main armhf libibverbs-dev armhf 22.1-1 [151 kB] Get: 192 http://deb.debian.org/debian buster/main armhf libjs-jquery all 3.3.1~dfsg-3 [332 kB] Get: 193 http://deb.debian.org/debian buster/main armhf libjs-underscore all 1.9.1~dfsg-1 [99.4 kB] Get: 194 http://deb.debian.org/debian buster/main armhf libjs-sphinxdoc all 1.8.4-1 [95.9 kB] Get: 195 http://deb.debian.org/debian buster/main armhf libkpathsea6 armhf 2018.20181218.49446-1 [157 kB] Get: 196 http://deb.debian.org/debian buster/main armhf liblapack3 armhf 3.8.0-2 [1631 kB] Get: 197 http://deb.debian.org/debian buster/main armhf liblapack-dev armhf 3.8.0-2 [1680 kB] Get: 198 http://deb.debian.org/debian buster/main armhf libmpich12 armhf 3.3-3 [1069 kB] Get: 199 http://deb.debian.org/debian buster/main armhf mpich armhf 3.3-3 [348 kB] Get: 200 http://deb.debian.org/debian buster/main armhf libmpich-dev armhf 3.3-3 [1364 kB] Get: 201 http://deb.debian.org/debian buster/main armhf libpmix2 armhf 3.1.2-3 [449 kB] Get: 202 http://deb.debian.org/debian buster/main armhf libopenmpi3 armhf 3.1.3-11 [1890 kB] Get: 203 http://deb.debian.org/debian buster/main armhf openmpi-common all 3.1.3-11 [165 kB] Get: 204 http://deb.debian.org/debian buster/main armhf openmpi-bin armhf 3.1.3-11 [198 kB] Get: 205 http://deb.debian.org/debian buster/main armhf libopenmpi-dev armhf 3.1.3-11 [964 kB] Get: 206 http://deb.debian.org/debian buster/main armhf libpaper-utils armhf 1.1.28 [17.6 kB] Get: 207 http://deb.debian.org/debian buster/main armhf libpotrace0 armhf 1.15-1 [23.9 kB] Get: 208 http://deb.debian.org/debian buster/main armhf libptexenc1 armhf 2018.20181218.49446-1 [58.1 kB] Get: 209 http://deb.debian.org/debian buster/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B] Get: 210 http://deb.debian.org/debian buster/main armhf libsynctex2 armhf 2018.20181218.49446-1 [67.4 kB] Get: 211 http://deb.debian.org/debian buster/main armhf libteckit0 armhf 2.5.8+ds2-5 [246 kB] Get: 212 http://deb.debian.org/debian buster/main armhf libtexlua52 armhf 2018.20181218.49446-1 [86.7 kB] Get: 213 http://deb.debian.org/debian buster/main armhf libtexlua53 armhf 2018.20181218.49446-1 [97.8 kB] Get: 214 http://deb.debian.org/debian buster/main armhf libtexluajit2 armhf 2018.20181218.49446-1 [201 kB] Get: 215 http://deb.debian.org/debian buster/main armhf libwoff1 armhf 1.0.2-1 [35.8 kB] Get: 216 http://deb.debian.org/debian buster/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB] Get: 217 http://deb.debian.org/debian buster/main armhf x11proto-dev all 2018.4-4 [251 kB] Get: 218 http://deb.debian.org/debian buster/main armhf x11proto-core-dev all 2018.4-4 [3128 B] Get: 219 http://deb.debian.org/debian buster/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.5 kB] Get: 220 http://deb.debian.org/debian buster/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.7 kB] Get: 221 http://deb.debian.org/debian buster/main armhf xtrans-dev all 1.3.5-1 [100 kB] Get: 222 http://deb.debian.org/debian buster/main armhf libxcb1-dev armhf 1.13.1-2 [171 kB] Get: 223 http://deb.debian.org/debian buster/main armhf libx11-dev armhf 2:1.6.7-1 [771 kB] Get: 224 http://deb.debian.org/debian buster/main armhf libxi6 armhf 2:1.7.9-1 [78.4 kB] Get: 225 http://deb.debian.org/debian buster/main armhf libxxhash0 armhf 0.6.5-2 [10.2 kB] Get: 226 http://deb.debian.org/debian buster/main armhf libzzip-0-13 armhf 0.13.62-3.2 [51.6 kB] Get: 227 http://deb.debian.org/debian buster/main armhf mscgen armhf 0.20-12 [45.8 kB] Get: 228 http://deb.debian.org/debian buster/main armhf preview-latex-style all 11.91-2 [201 kB] Get: 229 http://deb.debian.org/debian buster/main armhf python-alabaster all 0.7.8-1 [18.4 kB] Get: 230 http://deb.debian.org/debian buster/main armhf python-babel-localedata all 2.6.0+dfsg.1-1 [4083 kB] Get: 231 http://deb.debian.org/debian buster/main armhf python-pkg-resources all 40.8.0-1 [182 kB] Get: 232 http://deb.debian.org/debian buster/main armhf python-tz all 2019.1-1 [33.6 kB] Get: 233 http://deb.debian.org/debian buster/main armhf python-babel all 2.6.0+dfsg.1-1 [97.3 kB] Get: 234 http://deb.debian.org/debian buster/main armhf python-certifi all 2018.8.24-1 [140 kB] Get: 235 http://deb.debian.org/debian buster/main armhf python-chardet all 3.0.4-3 [80.6 kB] Get: 236 http://deb.debian.org/debian buster/main armhf python-roman all 2.0.0-3 [8688 B] Get: 237 http://deb.debian.org/debian buster/main armhf python-docutils all 0.14+dfsg-4 [379 kB] Get: 238 http://deb.debian.org/debian buster/main armhf python-idna all 2.6-1 [34.1 kB] Get: 239 http://deb.debian.org/debian buster/main armhf python-imagesize all 1.0.0-1 [4888 B] Get: 240 http://deb.debian.org/debian buster/main armhf python-markupsafe armhf 1.1.0-1 [13.6 kB] Get: 241 http://deb.debian.org/debian buster/main armhf python-jinja2 all 2.10-2 [106 kB] Get: 242 http://deb.debian.org/debian buster/main armhf python-pyparsing all 2.2.0+dfsg1-2 [89.5 kB] Get: 243 http://deb.debian.org/debian buster/main armhf python-six all 1.12.0-1 [15.7 kB] Get: 244 http://deb.debian.org/debian buster/main armhf python-packaging all 19.0-1 [20.4 kB] Get: 245 http://deb.debian.org/debian buster/main armhf python-pygments all 2.3.1+dfsg-1 [596 kB] Get: 246 http://deb.debian.org/debian buster/main armhf python-urllib3 all 1.24.1-1 [97.0 kB] Get: 247 http://deb.debian.org/debian buster/main armhf python-requests all 2.21.0-1 [67.1 kB] Get: 248 http://deb.debian.org/debian buster/main armhf python-typing all 3.6.6-1 [22.7 kB] Get: 249 http://deb.debian.org/debian buster/main armhf sphinx-common all 1.8.4-1 [500 kB] Get: 250 http://deb.debian.org/debian buster/main armhf python-sphinx all 1.8.4-1 [482 kB] Get: 251 http://deb.debian.org/debian buster/main armhf rdfind armhf 1.4.1-1 [36.3 kB] Get: 252 http://deb.debian.org/debian buster/main armhf symlinks armhf 1.4-3+b1 [10.7 kB] Get: 253 http://deb.debian.org/debian buster/main armhf t1utils armhf 1.41-3 [54.4 kB] Get: 254 http://deb.debian.org/debian buster/main armhf texlive-binaries armhf 2018.20181218.49446-1 [8656 kB] Get: 255 http://deb.debian.org/debian buster/main armhf xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 256 http://deb.debian.org/debian buster/main armhf texlive-base all 2018.20190227-2 [19.7 MB] Get: 257 http://deb.debian.org/debian buster/main armhf texlive-fonts-recommended all 2018.20190227-2 [5228 kB] Get: 258 http://deb.debian.org/debian buster/main armhf texlive-latex-base all 2018.20190227-2 [984 kB] Get: 259 http://deb.debian.org/debian buster/main armhf texlive-latex-recommended all 2018.20190227-2 [15.2 MB] Get: 260 http://deb.debian.org/debian buster/main armhf texlive-pictures all 2018.20190227-2 [8201 kB] Get: 261 http://deb.debian.org/debian buster/main armhf texlive-latex-extra all 2018.20190227-2 [12.3 MB] Get: 262 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Fetched 197 MB in 23s (8387 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:armhf. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_armhf.deb ... Unpacking libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_armhf.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_armhf.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_armhf.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:armhf. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_armhf.deb ... Unpacking libssl1.1:armhf (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_armhf.deb ... Unpacking libexpat1:armhf (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:armhf. Preparing to unpack .../14-libreadline7_7.0-5_armhf.deb ... Unpacking libreadline7:armhf (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:armhf. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_armhf.deb ... Unpacking libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_armhf.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:armhf. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_armhf.deb ... Unpacking libpython2-stdlib:armhf (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:armhf. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_armhf.deb ... Unpacking libpython-stdlib:armhf (2.7.16-1) ... Setting up libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20397 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_armhf.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20430 files and directories currently installed.) Preparing to unpack .../000-python_2.7.16-1_armhf.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package libfftw3-double3:armhf. Preparing to unpack .../001-libfftw3-double3_3.3.8-2_armhf.deb ... Unpacking libfftw3-double3:armhf (3.3.8-2) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../002-libpng16-16_1.6.36-6_armhf.deb ... Unpacking libpng16-16:armhf (1.6.36-6) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../003-libfreetype6_2.9.1-3+deb10u1_armhf.deb ... Unpacking libfreetype6:armhf (2.9.1-3+deb10u1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package ucf. Preparing to unpack .../005-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../006-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../007-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../008-libfontconfig1_2.13.1-2_armhf.deb ... Unpacking libfontconfig1:armhf (2.13.1-2) ... Selecting previously unselected package libde265-0:armhf. Preparing to unpack .../009-libde265-0_1.0.3-1+b1_armhf.deb ... Unpacking libde265-0:armhf (1.0.3-1+b1) ... Selecting previously unselected package libx265-165:armhf. Preparing to unpack .../010-libx265-165_2.9-4_armhf.deb ... Unpacking libx265-165:armhf (2.9-4) ... Selecting previously unselected package libheif1:armhf. Preparing to unpack .../011-libheif1_1.3.2-2~deb10u1_armhf.deb ... Unpacking libheif1:armhf (1.3.2-2~deb10u1) ... Selecting previously unselected package libjbig0:armhf. Preparing to unpack .../012-libjbig0_2.1-3.1+b2_armhf.deb ... Unpacking libjbig0:armhf (2.1-3.1+b2) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../013-libjpeg62-turbo_1%3a1.5.2-2+b1_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:1.5.2-2+b1) ... Selecting previously unselected package liblcms2-2:armhf. Preparing to unpack .../014-liblcms2-2_2.9-3_armhf.deb ... Unpacking liblcms2-2:armhf (2.9-3) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../015-libglib2.0-0_2.58.3-2+deb10u2_armhf.deb ... Unpacking libglib2.0-0:armhf (2.58.3-2+deb10u2) ... Selecting previously unselected package liblqr-1-0:armhf. Preparing to unpack .../016-liblqr-1-0_0.4.2-2.1_armhf.deb ... Unpacking liblqr-1-0:armhf (0.4.2-2.1) ... Selecting previously unselected package libltdl7:armhf. Preparing to unpack .../017-libltdl7_2.4.6-9_armhf.deb ... Unpacking libltdl7:armhf (2.4.6-9) ... Selecting previously unselected package libopenjp2-7:armhf. Preparing to unpack .../018-libopenjp2-7_2.3.0-2+deb10u1_armhf.deb ... Unpacking libopenjp2-7:armhf (2.3.0-2+deb10u1) ... Selecting previously unselected package libwebp6:armhf. Preparing to unpack .../019-libwebp6_0.6.1-2_armhf.deb ... Unpacking libwebp6:armhf (0.6.1-2) ... Selecting previously unselected package libtiff5:armhf. Preparing to unpack .../020-libtiff5_4.1.0+git191117-2~deb10u1_armhf.deb ... Unpacking libtiff5:armhf (4.1.0+git191117-2~deb10u1) ... Selecting previously unselected package libwebpmux3:armhf. Preparing to unpack .../021-libwebpmux3_0.6.1-2_armhf.deb ... Unpacking libwebpmux3:armhf (0.6.1-2) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../022-libxau6_1%3a1.0.8-1+b2_armhf.deb ... Unpacking libxau6:armhf (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../023-libxdmcp6_1%3a1.1.2-3_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-3) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../024-libxcb1_1.13.1-2_armhf.deb ... Unpacking libxcb1:armhf (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../025-libx11-data_2%3a1.6.7-1_all.deb ... Unpacking libx11-data (2:1.6.7-1) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../026-libx11-6_2%3a1.6.7-1_armhf.deb ... Unpacking libx11-6:armhf (2:1.6.7-1) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../027-libxext6_2%3a1.3.3-1+b2_armhf.deb ... Unpacking libxext6:armhf (2:1.3.3-1+b2) ... Selecting previously unselected package libicu63:armhf. Preparing to unpack .../028-libicu63_63.1-6+deb10u1_armhf.deb ... Unpacking libicu63:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../029-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package imagemagick-6-common. Preparing to unpack .../030-imagemagick-6-common_8%3a6.9.10.23+dfsg-2.1+deb10u1_all.deb ... Unpacking imagemagick-6-common (8:6.9.10.23+dfsg-2.1+deb10u1) ... Selecting previously unselected package libmagickcore-6.q16-6:armhf. Preparing to unpack .../031-libmagickcore-6.q16-6_8%3a6.9.10.23+dfsg-2.1+deb10u1_armhf.deb ... Unpacking libmagickcore-6.q16-6:armhf (8:6.9.10.23+dfsg-2.1+deb10u1) ... Selecting previously unselected package libmagickwand-6.q16-6:armhf. Preparing to unpack .../032-libmagickwand-6.q16-6_8%3a6.9.10.23+dfsg-2.1+deb10u1_armhf.deb ... Unpacking libmagickwand-6.q16-6:armhf (8:6.9.10.23+dfsg-2.1+deb10u1) ... Selecting previously unselected package poppler-data. Preparing to unpack .../033-poppler-data_0.4.9-2_all.deb ... Unpacking poppler-data (0.4.9-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../034-sgml-base_1.29_all.deb ... Unpacking sgml-base (1.29) ... Selecting previously unselected package tex-common. Preparing to unpack .../035-tex-common_6.11_all.deb ... Unpacking tex-common (6.11) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../036-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libprocps7:armhf. Preparing to unpack .../037-libprocps7_2%3a3.3.15-2_armhf.deb ... Unpacking libprocps7:armhf (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../038-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package procps. Preparing to unpack .../039-procps_2%3a3.3.15-2_armhf.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../040-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../041-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../042-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../043-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../044-libedit2_3.1-20181209-1_armhf.deb ... Unpacking libedit2:armhf (3.1-20181209-1) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../045-libkeyutils1_1.6-6_armhf.deb ... Unpacking libkeyutils1:armhf (1.6-6) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../046-libkrb5support0_1.17-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.17-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../047-libk5crypto3_1.17-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.17-3) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../048-libkrb5-3_1.17-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../049-libgssapi-krb5-2_1.17-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.17-3) ... Selecting previously unselected package openssh-client. Preparing to unpack .../050-openssh-client_1%3a7.9p1-10+deb10u2_armhf.deb ... Unpacking openssh-client (1:7.9p1-10+deb10u2) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../051-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../052-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../053-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../054-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... 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Setting up libtiff5:armhf (4.1.0+git191117-2~deb10u1) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up libde265-0:armhf (1.0.3-1+b1) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libwebpmux3:armhf (0.6.1-2) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up xdg-utils (1.1.3-1+deb10u1) ... Setting up chrpath (0.16-2+b1) ... Setting up libjsoncpp1:armhf (1.7.4-3) ... Setting up libsynctex2:armhf (2018.20181218.49446-1) ... Setting up libreadline7:armhf (7.0-5) ... Setting up libjs-underscore (1.9.1~dfsg-1) ... Setting up libpotrace0:armhf (1.15-1) ... Setting up x11proto-dev (2018.4-4) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libgfortran-8-dev:armhf (8.3.0-6) ... Setting up libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ... Setting up libice6:armhf (2:1.0.9-2) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up libxcb1:armhf (1.13.1-2) ... Setting up libxau-dev:armhf (1:1.0.8-1+b2) ... Setting up libwoff1:armhf (1.0.2-1) ... Setting up libtool (2.4.6-9) ... Setting up libarchive13:armhf (3.3.3-4+deb10u1) ... Setting up libxcb-render0:armhf (1.13.1-2) ... Setting up libfftw3-bin (3.3.8-2) ... Setting up libhwloc5:armhf (1.11.12-3) ... Setting up gfortran-8 (8.3.0-6) ... Setting up libedit2:armhf (3.1-20181209-1) ... Setting up libheif1:armhf (1.3.2-2~deb10u1) ... Setting up hwloc-nox (1.11.12-3) ... Setting up libavahi-common3:armhf (0.7-4+b1) ... Setting up libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Setting up m4 (1.4.18-2) ... Setting up libxcb-shm0:armhf (1.13.1-2) ... Setting up libhwloc-plugins:armhf (1.11.12-3) ... Setting up libllvm6.0:armhf (1:6.0.1-10) ... Setting up gfortran (4:8.3.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libclang1-6.0:armhf (1:6.0.1-10) ... Setting up libnl-route-3-200:armhf (3.4.0-1) ... Setting up libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ... Setting up libthai0:armhf (0.1.28-2) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libxdmcp-dev:armhf (1:1.1.2-3) ... Setting up libblas3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up doxygen (1.8.13-10) ... Setting up libptexenc1:armhf (2018.20181218.49446-1) ... Setting up libfreetype6:armhf (2.9.1-3+deb10u1) ... Setting up x11proto-core-dev (2018.4-4) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libjs-sphinxdoc (1.8.4-1) ... Setting up autoconf (2.69-11) ... Setting up libgvpr2 (2.40.1-6) ... Setting up dwz (0.12-3) ... Setting up libnl-3-dev:armhf (3.4.0-1) ... Setting up groff-base (1.22.4-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libcurl4:armhf (7.64.0-4+deb10u1) ... Setting up libx11-6:armhf (2:1.6.7-1) ... Setting up libharfbuzz0b:armhf (2.3.1-1) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up libfftw3-dev:armhf (3.3.8-2) ... Setting up libavahi-client3:armhf (0.7-4+b1) ... Setting up libblas-dev:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpaper1:armhf (1.1.28) ... Creating config file /etc/papersize with new version Setting up libibverbs1:armhf (22.1-1) ... Setting up liblapack3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libharfbuzz-icu0:armhf (2.3.1-1) ... Setting up libxcb1-dev:armhf (1.13.1-2) ... Setting up libxpm4:armhf (1:3.5.12-1) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libpmix2:armhf (3.1.2-3) ... Setting up ibverbs-providers:armhf (22.1-1) ... Setting up libpython2-stdlib:armhf (2.7.16-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up mpich (3.3-3) ... update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode Setting up openssh-client (1:7.9p1-10+deb10u2) ... Setting up libopenmpi3:armhf (3.1.3-11) ... Setting up libx11-dev:armhf (2:1.6.7-1) ... Setting up libxext6:armhf (2:1.3.3-1+b2) ... Setting up libpaper-utils (1.1.28) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up tex-common (6.11) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libnl-route-3-dev:armhf (3.4.0-1) ... Setting up libltdl-dev:armhf (2.4.6-9) ... Setting up libpython-stdlib:armhf (2.7.16-1) ... Setting up sphinx-common (1.8.4-1) ... Setting up liblapack-dev:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up libmpich-dev:armhf (3.3-3) ... update-alternatives: using /usr/include/arm-linux-gnueabihf/mpich to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Setting up libxt6:armhf (1:1.1.5-1+b3) ... Setting up libcups2:armhf (2.2.10-6+deb10u3) ... Setting up cmake (3.13.4-1) ... Setting up libhwloc-dev:armhf (1.11.12-3) ... Setting up libfontconfig1:armhf (2.13.1-2) ... Setting up python (2.7.16-1) ... Setting up openmpi-bin (3.1.3-11) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxmu6:armhf (2:1.1.2-2+b3) ... Setting up libxi6:armhf (2:1.7.9-1) ... Setting up python-typing (3.6.6-1) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up po-debconf (1.0.21) ... Setting up preview-latex-style (11.91-2) ... Setting up libpango-1.0-0:armhf (1.42.4-8~deb10u1) ... Setting up libxaw7:armhf (2:1.0.13-1+b2) ... Setting up libibverbs-dev:armhf (22.1-1) ... Setting up python-certifi (2018.8.24-1) ... Setting up python-pygments (2.3.1+dfsg-1) ... Setting up libcairo2:armhf (1.16.0-4) ... Setting up libcupsimage2:armhf (2.2.10-6+deb10u3) ... Setting up python-six (1.12.0-1) ... Setting up python-pyparsing (2.2.0+dfsg1-2) ... Setting up libmagickcore-6.q16-6:armhf (8:6.9.10.23+dfsg-2.1+deb10u1) ... Setting up python-imagesize (1.0.0-1) ... Setting up python-idna (2.6-1) ... Setting up libgd3:armhf (2.2.5-5.2) ... Setting up python-markupsafe (1.1.0-1) ... Setting up python-roman (2.0.0-3) ... Setting up python-tz (2019.1-1) ... Setting up python-alabaster (0.7.8-1) ... Setting up libmagickwand-6.q16-6:armhf (8:6.9.10.23+dfsg-2.1+deb10u1) ... Setting up python-chardet (3.0.4-3) ... Setting up python-babel (2.6.0+dfsg.1-1) ... update-alternatives: using /usr/bin/pybabel-python2 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up libopenmpi-dev:armhf (3.1.3-11) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Setting up libpangoft2-1.0-0:armhf (1.42.4-8~deb10u1) ... Setting up libpangocairo-1.0-0:armhf (1.42.4-8~deb10u1) ... Setting up python-packaging (19.0-1) ... Setting up python-urllib3 (1.24.1-1) ... Setting up libgs9:armhf (9.27~dfsg-2+deb10u3) ... Setting up mscgen (0.20-12) ... Setting up ghostscript (9.27~dfsg-2+deb10u3) ... Setting up python-jinja2 (2.10-2) ... Setting up libgvc6 (2.40.1-6) ... Setting up imagemagick-6.q16 (8:6.9.10.23+dfsg-2.1+deb10u1) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up texlive-binaries (2018.20181218.49446-1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up python-requests (2.21.0-1) ... Setting up texlive-base (2018.20190227-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex Setting up graphviz (2.40.1-6) ... Setting up texlive-latex-base (2018.20190227-2) ... Setting up texlive-latex-recommended (2018.20190227-2) ... Setting up texlive-pictures (2018.20190227-2) ... Setting up imagemagick (8:6.9.10.23+dfsg-2.1+deb10u1) ... Setting up texlive-fonts-recommended (2018.20190227-2) ... Setting up texlive-latex-extra (2018.20190227-2) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up debhelper (12.1.1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-4) ... Processing triggers for sgml-base (1.29) ... Setting up python-docutils (0.14+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python-sphinx (1.8.4-1) ... update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.11) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/gromacs-2019.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2019.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh_testdir dh_testroot rm -rf build docs/doxygen/*.pyc dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \ debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian debian/rules binary dh_testdir (mkdir -p build/basic; cd build/basic; cmake /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON) -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so -- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Found X11: /usr/lib/arm-linux-gnueabihf/libX11.so -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 1 -- Detected build CPU stepping - 1 -- Detected build CPU features - -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" -- Could not convert sample image, ImageMagick convert can not be used -- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.16", minimum required is "2.7") -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:229 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so -- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Found X11: /usr/lib/arm-linux-gnueabihf/libX11.so -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 1 -- Detected build CPU stepping - 1 -- Detected build CPU features - -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Could not convert sample image, ImageMagick convert can not be used -- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.16", minimum required is "2.7") -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/basic-dp (mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \ /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich") -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/mpicc.mpich -- Check for working C compiler: /usr/bin/mpicc.mpich -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 1 -- Detected build CPU stepping - 1 -- Detected build CPU features - -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi.mpich" -- Using manually set library suffix: "_mpi.mpich" -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/mpich (mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \ /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich") -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/mpicc.mpich -- Check for working C compiler: /usr/bin/mpicc.mpich -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:229 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 1 -- Detected build CPU stepping - 1 -- Detected build CPU features - -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi_d.mpich" -- Using manually set library suffix: "_mpi_d.mpich" -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/mpich-dp (mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \ /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi") -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/mpicc.openmpi -- Check for working C compiler: /usr/bin/mpicc.openmpi -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 1 -- Detected build CPU stepping - 1 -- Detected build CPU features - -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi.openmpi" -- Using manually set library suffix: "_mpi.openmpi" -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/openmpi (mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \ /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi") -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/mpicc.openmpi -- Check for working C compiler: /usr/bin/mpicc.openmpi -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:229 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 1 -- Detected build CPU stepping - 1 -- Detected build CPU features - -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi_d.openmpi" -- Using manually set library suffix: "_mpi_d.openmpi" -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/openmpi-dp touch configure-stamp dh_testdir /usr/bin/make -j3 -C build/basic make[1]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic/CMakeFiles /build/gromacs-2019.1/build/basic/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c Scanning dependencies of target libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c 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cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/comm.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/reduce.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/event.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/event.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/reduce_fast.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/gather.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/scatter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/group.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/group.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_init.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/topology.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/list.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/list.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/type.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/type.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/scan.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/numa_malloc.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/once.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 4%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 4%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs /build/gromacs-2019.1/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 5%] Built target mdrun_objlib /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs /build/gromacs-2019.1/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp Scanning dependencies of target view_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /build/gromacs-2019.1/src/programs/view/3dview.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 7%] Built target tng_io_obj /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /build/gromacs-2019.1/src/programs/view/buttons.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /build/gromacs-2019.1/src/programs/view/dialogs.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp Scanning dependencies of target mdrun_test_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/energyreader.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /build/gromacs-2019.1/src/programs/view/fgrid.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /build/gromacs-2019.1/src/programs/view/filter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /build/gromacs-2019.1/src/programs/view/manager.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 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/usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /build/gromacs-2019.1/src/programs/view/xmb.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/terminationhelper.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /build/gromacs-2019.1/src/programs/view/xutil.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 8%] Built target view_objlib cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/trajectoryreader.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 8%] Built target mdrun_test_objlib cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused 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/build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/scanner.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/scanner.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/parser.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/parser.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 24%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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&& /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomset.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o 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/build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/units.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/observableshistory.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpformat.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpmanager.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helptopic.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/rstparser.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/boxutilities.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/mshift.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc-simd.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/rmpbc.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/seed.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/forcetable.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 CubicSplineTable::CubicSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/cyclecounter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/wallcycle.cpp /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 QuadraticSplineTable::QuadraticSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 std::vector thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing)); ^ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/walltime_accounting.cpp /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'std::vector gmx::internal::vectorSecondDerivative(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 vectorSecondDerivative(ArrayRef f, double spacing) ^~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomprop.cpp /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef, gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 throwUnlessDerivativeIsConsistentWithFunction(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atoms.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomsbuilder.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/block.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/exclusionblocks.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/forcefieldparameters.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/idef.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/ifunc.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/index.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/invblock.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/mtop_util.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/residuetypes.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/symtab.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/topology.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/topsort.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/alignedallocator.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/basenetwork.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o 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-I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/g96io.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmx_internal_xdr.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio-xdr.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/groio.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.h:44, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector gmx_fio_get_output_file_positions()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/libxdrf.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/matio.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/md5.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/mtxio.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/oenv.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/timecontrol.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/warninp.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/writeps.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xdrd.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xtcio.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xvgr.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/__/external/vmd_molfile/vmddlopen.c.o -c /build/gromacs-2019.1/src/external/vmd_molfile/vmddlopen.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/output.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull_rotation.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/awh.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/bias.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void Bias::updateForceCorrelationGrid(gmx::ArrayRef probWeightNeighbor, ^~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:70: /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 updateForceCorrelationGrid(probWeightNeighbor, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tempForce_, biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biassharing.cpp /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.h:53, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biaswriter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef, const gmx::BiasParams&)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void updateTargetDistribution(gmx::ArrayRef pointState, ^~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector&, const gmx::Grid&, int, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::calcUmbrellaForceAndPotential(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::calcConvolvedForce(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:463:38: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forceFromNeighbor); ~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::moveUmbrella(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:487:38: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 CoordState::sampleUmbrellaGridpoint(const Grid &grid, ^~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleProbabilityWeights(const Grid &grid, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleCoordAndPmf(const Grid &grid, ^~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector*)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/grid.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef, bool, double)': /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void CorrelationTensor::addData(double weight, ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector&, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSize(const BiasParams ¶ms, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/pointstate.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/read-params.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/support.cpp /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector&, const gmx::AwhDimParams*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imd.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imdsocket.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/anadih.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/binsearch.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/cmat.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/dens_filter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/dlist.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/eigio.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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/build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/sm_distance.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/sm_insolidangle.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/sm_keywords.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/sm_merge.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/sm_permute.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/sm_position.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/sm_same.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/sm_simple.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/symrec.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysissettings.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/angle.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/distance.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysismodule.h:49, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.h:45, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/pairdist.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 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-std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src 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-DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/options.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsassigner.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsection.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsvisitor.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/timeunitmanager.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate::ValueList*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/treesupport.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/manager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/taskassignment.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectory/energyframe.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectory/trajectoryframe.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /build/gromacs-2019.1/src/gromacs/mimic/MimicUtils.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/gromacs-2019.1/build/basic/src/gromacs/utility/baseversion-gen.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.h:39, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef >, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs.so.4 -o ../../lib/libgromacs.so.4.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp -Wl,-rpath,:::::::::::::::::::::::::::::::::: /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -fopenmp -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.4.0.0 ../../lib/libgromacs.so.4 ../../lib/libgromacs.so make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 98%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/share/template /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/share/template /build/gromacs-2019.1/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 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/build/gromacs-2019.1/share/template/template.cpp Scanning dependencies of target gmx make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/gmx.dir/gmx.cpp.o -c /build/gromacs-2019.1/src/programs/gmx.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src 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CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib: ../../lib/libgromacs.so.4.0.0 -fopenmp /usr/lib/arm-linux-gnueabihf/libX11.so -lm cd /build/gromacs-2019.1/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../lib/libgromacs.so.4.0.0 -fopenmp -lm make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target template make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target gmx make[2]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic/CMakeFiles 0 make[1]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -j3 -C build/basic-dp make[1]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles /build/gromacs-2019.1/build/basic-dp/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build Scanning dependencies of target libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/scan.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/numa_malloc.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/once.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 4%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 4%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 5%] Built target mdrun_objlib /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scanning dependencies of target view_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /build/gromacs-2019.1/src/programs/view/3dview.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /build/gromacs-2019.1/src/programs/view/buttons.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /build/gromacs-2019.1/src/programs/view/dialogs.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 7%] Built target tng_io_obj /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /build/gromacs-2019.1/src/programs/view/fgrid.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /build/gromacs-2019.1/src/programs/view/filter.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp Scanning dependencies of target mdrun_test_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/energyreader.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /build/gromacs-2019.1/src/programs/view/logo.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /build/gromacs-2019.1/src/programs/view/manager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp /build/gromacs-2019.1/src/programs/view/manager.cpp: In function 'bool ManCallBack(t_x11*, XEvent*, Window, void*)': /build/gromacs-2019.1/src/programs/view/manager.cpp:371:46: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 put_atoms_in_compact_unitcell(man->molw->ePBC, ecenterDEF, man->box, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atomsArrayRef); ~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/programs/view/manager.cpp:371:46: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /build/gromacs-2019.1/src/programs/view/molps.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /build/gromacs-2019.1/src/programs/view/nleg.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /build/gromacs-2019.1/src/programs/view/nmol.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /build/gromacs-2019.1/src/programs/view/popup.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /build/gromacs-2019.1/src/programs/view/xutil.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 8%] Built target view_objlib cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/trajectoryreader.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 8%] Built target mdrun_test_objlib cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 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/usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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/usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/scanner.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/scanner.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/parser.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/parser.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 24%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 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/build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/filenm.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/pargs.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/shellcompletions.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/viewit.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/atomdistribution.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/box.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/cellsizes.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp /build/gromacs-2019.1/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef >, tmpi_comm_* const*, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:235:13: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 static void low_set_ddbox(int numPbcDimensions, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef >, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void set_ddbox(const gmx_domdec_t &dd, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 low_set_ddbox(dd.npbcdim, dd.numBoundedDimensions, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &dd.nc, box, calculateUnboundedSize, xRef, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddbox); ~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef >, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:308:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void set_ddbox_cr(const t_commrec &cr, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:317:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dd_nc, box, true, x, nullptr, ddbox); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/distribute.cpp /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef >, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void dd_collect_vec(gmx_domdec_t *dd, ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)': /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:310:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->x), globalXRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:315:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->v), globalVRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:320:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->cg_p), globalCgpRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlb.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlbtiming.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_constraints.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(const gmx_domdec_t *dd, ^~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef, gmx::ArrayRef) [with T = gmx::BasicVector]': /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_setup.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const t_state&, real)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:3015:14: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, false, state.box, true, state.x, &ddbox); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_specatomcomm.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void set_dd_limits_and_grid(const gmx::MDLogger&, t_commrec*, gmx_domdec_t*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef >, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2137:13: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 static void set_dd_limits_and_grid(const gmx::MDLogger &mdlog, ^~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2358:21: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox_cr(*cr, &dd->nc, *ir, box, xGlobal, ddbox); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2383:21: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox_cr(*cr, nullptr, *ir, box, xGlobal, ddbox); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_topology.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'gmx_domdec_t* init_domain_decomposition(const gmx::MDLogger&, t_commrec*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef >, gmx::LocalAtomSetManager*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2953:15: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 gmx_domdec_t *init_domain_decomposition(const gmx::MDLogger &mdlog, ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2979:27: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_dd_limits_and_grid(mdlog, cr, dd, options, mdrunOptions, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mtop, ir, ~~~~~~~~~ box, xGlobal, ~~~~~~~~~~~~~ &ddbox); ~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_vsite.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(dd, d, dddirBackward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(dd, d, dddirForward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, real (*)[3], gmx::ArrayRef >, gmx_wallcycle*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:296:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void dd_move_x(gmx_domdec_t *dd, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 ddSendrecv(dd, d, dddirBackward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ArrayRef >, real (*)[3], gmx_wallcycle*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:408:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void dd_move_f(gmx_domdec_t *dd, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 ddSendrecv(dd, d, dddirForward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dump.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/ga2la.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomset.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetdata.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/redistribute.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/utility.cpp /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)': /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(dd, d, dddirBackward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ gmx::arrayRefFromArray(&buf_s[0].min0, numReals), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gmx::arrayRefFromArray(&buf_r[0].min0, numReals)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/utility.h:45, from /build/gromacs-2019.1/src/gromacs/domdec/utility.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/utility.h:45, from /build/gromacs-2019.1/src/gromacs/domdec/utility.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, gmx::PaddedVector >*, int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/3dtransforms.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/do_fit.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/functions.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/invertmatrix.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/units.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/utilities.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/veccompare.cpp /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, gmx::PaddedVector >*)': /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 ddSendrecv(dd, dim_ind, dddirBackward, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ work.positionBuffer, rvecBufferRef); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/vecdump.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/df_history.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/iforceprovider.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/inputrec.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/md_enums.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/observableshistory.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t*, const t_inputrec*, t_state*, gmx::PaddedVector >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)': /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3244:18: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, true, ~~~~~~~~~^~~~~~~~~~~ DDMASTER(dd) ? state_global->box : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ true, xGlobal, ~~~~~~~~~~~~~~ &ddbox); ~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3297:18: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, bMasterState, state_local->box, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ true, state_local->x, &ddbox); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3316:18: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, bMasterState, state_local->box, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bNStGlobalComm, state_local->x, &ddbox); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_local->x); ~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_local->x); ~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3419:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid(fr->nbv->nbs.get(), fr->ePBC, state_local->box, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, ~~ comm->zones.size[0].bb_x0, ~~~~~~~~~~~~~~~~~~~~~~~~~~ comm->zones.size[0].bb_x1, ~~~~~~~~~~~~~~~~~~~~~~~~~~ comm->updateGroupsCog.get(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, dd->ncg_home, ~~~~~~~~~~~~~~~~ comm->zones.dens_zone0, ~~~~~~~~~~~~~~~~~~~~~~~ fr->cginfo, ~~~~~~~~~~~ state_local->x, ~~~~~~~~~~~~~~~ ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->nbv->grp[eintLocal].kernel_type, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->nbv->nbat); ~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef >, gmx::index))[3]': /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:207:7: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 rvec *makeRvecArray(gmx::ArrayRef v, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpformat.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpmanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helptopic.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/rstparser.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/boxutilities.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/mshift.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc-simd.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/rmpbc.cpp /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1413:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef x) ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1473:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/seed.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/forcetable.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 CubicSplineTable::CubicSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 QuadraticSplineTable::QuadraticSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 std::vector thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing)); ^ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/cyclecounter.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/wallcycle.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/walltime_accounting.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomprop.cpp /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'std::vector gmx::internal::vectorSecondDerivative(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 vectorSecondDerivative(ArrayRef f, double spacing) ^~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef, gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 throwUnlessDerivativeIsConsistentWithFunction(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atoms.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomsbuilder.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/block.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/exclusionblocks.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/forcefieldparameters.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/idef.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/ifunc.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/index.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/invblock.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/mtop_util.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/residuetypes.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/symtab.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/topology.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/topsort.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/alignedallocator.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/basenetwork.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/baseversion.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/binaryinformation.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/compare.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include 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CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/filetypes.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/g96io.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmx_internal_xdr.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio-xdr.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/groio.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.h:44, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector gmx_fio_get_output_file_positions()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/libxdrf.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/matio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/md5.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/mtxio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/oenv.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/pdbio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/readinp.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/timecontrol.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tpxio.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.h:42, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.h:42, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trrio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trxio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/vmdio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/warninp.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/writeps.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xdrd.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xtcio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xvgr.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/__/external/vmd_molfile/vmddlopen.c.o -c /build/gromacs-2019.1/src/external/vmd_molfile/vmddlopen.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp:51: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/output.cpp /usr/include/c++/8/bits/vector.tcc: In function 'void init_swapcoords(FILE*, t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const MdrunOptions&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull_rotation.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp:46: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::unique_ptr ed_open(int, ObservablesHistory*, const char*, const char*, gmx_bool, const gmx_output_env_t*, const t_commrec*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef >, const t_pbc&, int, real)': /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:950:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 bool pullCheckPbcWithinGroup(const pull_t &pull, ^~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 } ^ /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/awh.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/bias.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void Bias::updateForceCorrelationGrid(gmx::ArrayRef probWeightNeighbor, ^~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:70: /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 updateForceCorrelationGrid(probWeightNeighbor, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tempForce_, biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.h:53, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biassharing.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biaswriter.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef, const gmx::BiasParams&)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void updateTargetDistribution(gmx::ArrayRef pointState, ^~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector&, const gmx::Grid&, int, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::calcUmbrellaForceAndPotential(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::calcConvolvedForce(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:463:38: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forceFromNeighbor); ~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::moveUmbrella(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:487:38: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleProbabilityWeights(const Grid &grid, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleCoordAndPmf(const Grid &grid, ^~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 CoordState::sampleUmbrellaGridpoint(const Grid &grid, ^~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector*)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/grid.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef, bool, double)': /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void CorrelationTensor::addData(double weight, ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/pointstate.cpp /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector&, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSize(const BiasParams ¶ms, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/read-params.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/support.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector&, const gmx::AwhDimParams*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imd.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imdsocket.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/anadih.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/binsearch.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/cmat.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/dens_filter.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/dlist.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/eigio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/fitahx.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_anadock.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_anadock.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_analyze.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_angle.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_awh.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_bar.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/commandline/pargs.h:47, from /build/gromacs-2019.1/src/gromacs/gmxana/gmx_awh.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_bundle.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/commandline/pargs.h:47, from /build/gromacs-2019.1/src/gromacs/gmxana/gmx_awh.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In function 'int gmx_awh(int, char**)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_chi.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_cluster.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_confrms.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_covar.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_current.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_density.cpp cd 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-D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_rotmat.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_saltbr.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_sans.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_saxs.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_sham.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_sorient.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_spatial.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_spol.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_traj.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjcat.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_trjcat.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjconv.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_trjconv.cpp /build/gromacs-2019.1/src/gromacs/gmxana/gmx_trjconv.cpp: In function 'int gmx_trjconv(int, char**)': /build/gromacs-2019.1/src/gromacs/gmxana/gmx_trjconv.cpp:1702:66: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ positionsArrayRef); ~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gmxana/gmx_trjconv.cpp:1702:66: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/gmxana/gmx_trjconv.cpp:373:50: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gmxana/gmx_trjconv.cpp:373:50: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/gmxana/gmx_trjconv.cpp:316:46: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gmxana/gmx_trjconv.cpp:316:46: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_tune_pme.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_tune_pme.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_velacc.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_wham.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_wheel.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/hxprops.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/nrama.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/nsfactor.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/powerspect.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/pp2shift.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/princ.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/sfactor.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/add_par.cpp /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcZeroPointEnergy(gmx::ArrayRef, real)': /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double calcZeroPointEnergy(gmx::ArrayRef eigval, ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalInternalEnergy(gmx::ArrayRef, real, gmx_bool, real)': /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp:67:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double calcVibrationalInternalEnergy(gmx::ArrayRef eigval, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalHeatCapacity(gmx::ArrayRef, real, gmx_bool, real)': /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp:99:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double calcVibrationalHeatCapacity(gmx::ArrayRef eigval, ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcQuasiHarmonicEntropy(gmx::ArrayRef, real, gmx_bool, real)': /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp:174:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double calcQuasiHarmonicEntropy(gmx::ArrayRef eigval, ^~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcSchlitterEntropy(gmx::ArrayRef, real, gmx_bool)': /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.cpp:206:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double calcSchlitterEntropy(gmx::ArrayRef eigval, ^~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/calch.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/convparm.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/gen_ad.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/topology/block.h:42, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/grompp-impl.h:42, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/convparm.h:41, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/convparm.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/topology/block.h:42, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/grompp-impl.h:42, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/convparm.h:41, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/convparm.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'int enter_params(gmx_ffparams_t*, t_functype, real*, int, real, int, bool)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/genconf.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/genhydro.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/gmxcpp.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/gpp_nextnb.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/grompp.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/h_db.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert-molecules.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/insert-molecules.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/keyvaluetreemdpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/keyvaluetreemdpwriter.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector makeExclusionDistances(const t_atoms*, gmx_atomprop_t, real, real)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/readir.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/readpull.cpp /build/gromacs-2019.1/src/gromacs/gmxpreprocess/readpull.cpp: In function 'pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)': /build/gromacs-2019.1/src/gromacs/gmxpreprocess/readpull.cpp:537:36: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 pullCheckPbcWithinGroup(*pull_work, ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ gmx::arrayRefFromArray(reinterpret_cast(x), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mtop->natoms), ~~~~~~~~~~~~~~ pbc, g, c_pullGroupSmallGroupThreshold); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gmxpreprocess/readpull.cpp:564:40: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 pullCheckPbcWithinGroup(*pull_work, ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ gmx::arrayRefFromArray(reinterpret_cast(x), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mtop->natoms), ~~~~~~~~~~~~~~ pbc, g, c_pullGroupPbcMargin); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/readrot.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/resall.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/solvate.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/solvate.cpp:44: /usr/include/c++/8/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/specbond.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/gmxpreprocess/solvate.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In function 'int gmx_solvate(int, char**)': /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 _M_range_insert(__pos, __first, __last, ^~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/topio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/toppush.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/topshake.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/toputil.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/x2top.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/xlate.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/autocorr.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/crosscorr.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/expfit.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/commandline/pargs.h:47, from /build/gromacs-2019.1/src/gromacs/correlationfunctions/autocorr.h:53, from /build/gromacs-2019.1/src/gromacs/correlationfunctions/autocorr.cpp:46: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/commandline/pargs.h:47, from /build/gromacs-2019.1/src/gromacs/correlationfunctions/autocorr.h:53, from /build/gromacs-2019.1/src/gromacs/correlationfunctions/autocorr.cpp:46: /usr/include/c++/8/bits/stl_vector.h: In function 'void low_do_four_core(int, real*, real*, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/gmx_lmcurve.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/integrate.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/polynomials.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /build/gromacs-2019.1/src/gromacs/statistics/statistics.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/abstractdata.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/correlationfunctions/manyautocorrelation.h:47, from /build/gromacs-2019.1/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/correlationfunctions/manyautocorrelation.h:47, from /build/gromacs-2019.1/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In function '_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'int many_auto_correl(std::vector >*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/analysisdata.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/arraydata.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/dataframe.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/datamodule.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/datamodulemanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/analysisdata/arraydata.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/arraydata.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/dataproxy.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/average.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/displacement.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/frameaverager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/analysisdata/dataframe.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/displacement.cpp:46: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.cpp:610:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 AnalysisDataStorageFrameData::addPointSet(int dataSetIndex, int firstColumn, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()': /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.cpp:750:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 data_->addPointSet(currentDataSet_, firstColumn, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ makeConstArrayRef(values_). ~~~~~~~~~~~~~~~~~~~~~~~~~~~ subArray(begin, end-begin)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.cpp:750:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/lifetime.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/plot.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/centerofmass.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/compiler.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/evaluate.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/indexutil.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/mempool.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/nbsearch.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/params.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/parsetree.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/poscalc.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/position.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/scanner_internal.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/selection.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/selection/selection.h:47, from /build/gromacs-2019.1/src/gromacs/selection/selection.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/selection/selection.h:47, from /build/gromacs-2019.1/src/gromacs/selection/selection.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector*, std::vector*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/selection/selection.h:47, from /build/gromacs-2019.1/src/gromacs/selection/selection.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/selection/selection.h:47, from /build/gromacs-2019.1/src/gromacs/selection/selection.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/selectioncollection.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/selectionoption.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/selectionoptionmanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include 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-std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysismodule.h:49, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.h:45, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/pairdist.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysismodule.h:49, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.h:45, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysismodule.h:49, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.h:45, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/select.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/trajectory.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/runnercommon.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/topologyinformation.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /build/gromacs-2019.1/src/gromacs/tools/check.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /build/gromacs-2019.1/src/gromacs/tools/convert_tpr.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /build/gromacs-2019.1/src/gromacs/tools/dump.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/report-methods.cpp.o -c /build/gromacs-2019.1/src/gromacs/tools/report-methods.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/chargegroup.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/conformation-utilities.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/network.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nrnb.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_generic.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic_cg.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_generic_cg.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nonbonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nonbonded.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/boxdeformation.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/calc_verletbuf.cpp /build/gromacs-2019.1/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef >, real (*)[3], int64_t)': /build/gromacs-2019.1/src/gromacs/mdlib/boxdeformation.cpp:109:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 BoxDeformation::apply(ArrayRef x, ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/calcmu.cpp /build/gromacs-2019.1/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef >, const real*, const real*, int, double*, double*)': /build/gromacs-2019.1/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void calc_mu(int start, int homenr, gmx::ArrayRef x, const real q[], const real qB[], ^~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/calcvir.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/mdlib/calc_verletbuf.h:39, from /build/gromacs-2019.1/src/gromacs/mdlib/calc_verletbuf.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector get_verlet_buffer_atomtypes(const gmx_mtop_t*, bool, int*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/checkpointhandler.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.h:48, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.h:48, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/compute_io.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/constr.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/constraintrange.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/coupling.cpp /build/gromacs-2019.1/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef, gmx_bool, int, int, int, int*, real, real, real*, int*)': /build/gromacs-2019.1/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 static void constr_recur(const t_blocka *at2con, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef, gmx::FlexibleConstraintTreatment)': /build/gromacs-2019.1/src/gromacs/mdlib/constr.cpp:848:10: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 t_blocka make_at2con(const gmx_moltype_t &moltype, ^~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ebin.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/expanded.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/force.cpp /build/gromacs-2019.1/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef >, real, const gmx_bool*, const real*)': /build/gromacs-2019.1/src/gromacs/mdlib/coupling.cpp:781:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void andersen_tcoupl(const t_inputrec *ir, int64_t step, ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/force.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef, t_lambda*)': /build/gromacs-2019.1/src/gromacs/mdlib/force.cpp:698:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void sum_dhdl(gmx_enerdata_t *enerd, gmx::ArrayRef lambda, t_lambda *fepvals) ^~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/forcerec.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/groupcoord.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/lincs.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/md_support.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin_bar.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, gmx_mtop_t*, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void mdoutf_write_to_trajectory_files(FILE *fplog, const t_commrec *cr, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:269:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->x), globalXRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:274:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->v), globalVRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:280:27: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state_local, f_local, gmx::arrayRefFromArray(reinterpret_cast(f_global), f_local.size())); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdsetup.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/membed.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_atomdata.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid(nbnxn_search_t, int, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, int, int, real, const int*, gmx::ArrayRef >, int, const int*, int, nbnxn_atomdata_t*)': /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp:1416:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void nbnxn_put_on_grid(nbnxn_search_t nbs, ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nbnxn_search_t, const gmx_domdec_zones_t*, const int*, gmx::ArrayRef >, int, nbnxn_atomdata_t*)': /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp:1520:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs, ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp:1536:26: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid(nbs, nbs->ePBC, nullptr, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ zone, c0, c1, ~~~~~~~~~~~~~ nullptr, ~~~~~~~~ zones->cg_range[zone], ~~~~~~~~~~~~~~~~~~~~~~ zones->cg_range[zone+1], ~~~~~~~~~~~~~~~~~~~~~~~~ -1, ~~~ atinfo, ~~~~~~~ x, ~~ 0, nullptr, ~~~~~~~~~~~ nb_kernel_type, ~~~~~~~~~~~~~~~ nbat); ~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nsgrid.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/perf_est.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gamess.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gaussian.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_mopac.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_orca.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qmmm.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 int add_binr(t_bin *b, gmx::ArrayRef r) ^~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void extract_binr(t_bin *b, int index, gmx::ArrayRef r) ^~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/resethandler.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rf_util.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/settle.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/shake.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/sighandler.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/simulationsignal.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx_bool, int, gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, t_state*, gmx::ArrayRefWithPadding >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, const gmx_groups_t*, gmx_shellfc_t*, t_forcerec*, gmx::PpForceWorkload*, double, real*, const gmx_vsite_t*, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:1144:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdstep, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forceWithPadding[Min], force_vir, md, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:1254:17: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1, nrnb, wcycle, ~~~~~~~~~~~~~~~~ top, groups, state->box, posWithPadding[Try], &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forceWithPadding[Try], force_vir, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ md, enerd, fcd, state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shellfc_flags, ~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/splitter.cpp /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void computeSpecialForces(FILE*, const t_commrec*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, double, gmx_wallcycle_t, ForceProviders*, real (*)[3], gmx::ArrayRef >, const t_mdatoms*, real*, int, gmx::ForceWithVirial*, gmx_enerdata_t*, gmx_edsam*, gmx_bool)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:796:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 computeSpecialForces(FILE *fplog, ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2721:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef x) ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, t_nrnb*, gmx_wallcycle_t, gmx_localtop_t*, const gmx_groups_t*, real (*)[3], gmx::ArrayRefWithPadding >, history_t*, gmx::ArrayRefWithPadding >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef, t_graph*, t_forcerec*, gmx::PpForceWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2119:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void do_force(FILE *fplog, ^~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1175:30: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid(nbv->nbs.get(), fr->ePBC, box, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, vzero, box_diag, ~~~~~~~~~~~~~~~~~~~ nullptr, 0, mdatoms->homenr, -1, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->cginfo, x.unpaddedArrayRef(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, nullptr, ~~~~~~~~~~~ nbv->grp[eintLocal].kernel_type, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nbv->nbat); ~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid_nonlocal(nbv->nbs.get(), domdec_zones(cr->dd), ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->cginfo, x.unpaddedArrayRef(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nbv->grp[eintNonlocal].kernel_type, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nbv->nbat); ~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1575:25: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation, ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, t, wcycle, ~~~~~~~~~~~~~~~~ fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ flags, &forceWithVirial, enerd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ed, bNS); ~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1626:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2047:25: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation, ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, t, wcycle, ~~~~~~~~~~~~~~~~ fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ flags, &forceWithVirial, enerd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ed, bNS); ~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2058:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2069:26: note: parameter passing for argument of type 'const gmx::ArrayRef >' changed in GCC 7.1 dd_move_f(cr->dd, forceWithVirial.force_, nullptr, wcycle); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/stat.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/stophandler.cpp /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void initialize_lambdas(FILE*, t_inputrec*, int*, gmx::ArrayRef, double*)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2874:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef lambda, double *lam0) ^~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void init_md(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, double*, double*, t_state*, double*, t_nrnb*, gmx_mtop_t*, gmx_update_t**, gmx::BoxDeformation*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, real (*)[3], real (*)[3], real (*)[3], real (*)[3], real*, gmx_bool*, t_vcm**, gmx_wallcycle_t)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void init_rerun(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, t_state*, double*, t_nrnb*, gmx_mtop_t*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tgroup.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, t_mdebin*, gmx_ekindata_t*, gmx::ArrayRef >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)': /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp:57:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(FILE *fplog, ^~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp:164:41: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, t, state, state_global, observablesHistory, f); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/updategroups.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector&}; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], t_state*, t_nrnb*, gmx_update_t*)': /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:1781:27: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 upd->deform->apply(localX, state->box, step); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef >, const gmx_update_t*, const gmx::Constraints*)': /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:1920:17: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 extern gmx_bool update_randomize_velocities(const t_inputrec *ir, int64_t step, const t_commrec *cr, ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:1944:24: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 andersen_tcoupl(ir, step, cr, md, v, rate, ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ upd->sd->randomize_group, upd->sd->boltzfac); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp:85:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void UpdateGroupsCog::addCogs(gmx::ArrayRef globalAtomIndices, ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp:45: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/update.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/update.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function 'void update_realloc(gmx_update_t*, int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/vcm.cpp /usr/include/c++/8/bits/stl_vector.h: In function 'gmx_update_t* init_update(const t_inputrec*, gmx::BoxDeformation*)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/wall.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/wnblist.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/bonded.cpp /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp:758:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void constructVsitesGlobal(const gmx_mtop_t &mtop, ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.h:44, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/disre.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.h:44, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.3': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/gpubonded-impl.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/listed-forces.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-internal.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/listed-internal.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/manage-threading.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/manage-threading.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/orires.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/orires.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/pairs.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/pairs.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/position-restraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/position-restraints.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/restcbt.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/restcbt.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/calculate-spline-moduli.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/ewald.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald-utils.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/ewald-utils.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/long-range-correction.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gather.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-grid.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-load-balancing.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-pp.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-redistribute.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-solve.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spline-work.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = gmx::BasicVector]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spread.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program-impl.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/calcgrid.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft5d.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/parallel_3dfft.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft_fftw3.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/cpuinfo.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/detecthardware.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/gpu_hw_info.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/hardwaretopology.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/printhardware.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/integrator.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/integrator.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/logging.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/multisim.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/replicaexchange.cpp /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &state->s, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->f); ~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:564:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, &state->s, makeArrayRef(state->s.x), globalXRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:869:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, nullptr, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ count, nrnb, wcycle, top, &top_global->groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ems->s.lambda, graph, fr, ppForceWorkload, vsite, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bNS ? GMX_FORCE_NS : 0), ~~~~~~~~~~~~~~~~~~~~~~~~~ DOMAINDECOMP(cr) ? ~~~~~~~~~~~~~~~~~~ DdOpenBalanceRegionBeforeForceComputation::yes : ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdOpenBalanceRegionBeforeForceComputation::no, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DOMAINDECOMP(cr) ? ~~~~~~~~~~~~~~~~~~ DdCloseBalanceRegionAfterForceComputation::yes : ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdCloseBalanceRegionAfterForceComputation::no); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:936:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_md()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:875:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bNS ? GMX_FORCE_NS : 0) | force_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1026:25: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1051:33: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ir, state, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, fr, ~~~~~~~~~~~~~~~ outf, mdebin, ekind, f, ~~~~~~~~~~~~~~~~~~~~~~~ checkpointHandler->isCheckpointingStep(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bRerunMD, bLastStep, ~~~~~~~~~~~~~~~~~~~~ mdrunOptions.writeConfout, ~~~~~~~~~~~~~~~~~~~~~~~~~~ bSumEkinhOld); ~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1089:55: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, upd, constr); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1292:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, const gmx_multisim_t*, gmx::IMDOutputProvider*, t_inputrec*, const MdrunOptions&, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t**, t_nrnb*, real*, t_forcerec*, gmx_enerdata_t**, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, nullptr); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_lbfgs()': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:1932:41: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), &ems.s, state_global, observablesHistory, ems.f); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_rerun()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:582:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, ir, awh, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, ed, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_NS | force_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:599:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ir, state, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, fr, ~~~~~~~~~~~~~~~ outf, mdebin, ekind, f, ~~~~~~~~~~~~~~~~~~~~~~~ isCheckpointingStep, doRerun, isLastStep, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdrunOptions.writeConfout, ~~~~~~~~~~~~~~~~~~~~~~~~~~ bSumEkinhOld); ~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:663:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:53: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, const gmx::PaddedVector >*, em_state_t*, gmx::Constraints*, int64_t)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_cg()': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &state->s, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->f); ~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:53: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_mimic()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:465:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, ir, awh, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, ed, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_NS | force_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:482:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ir, state, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, fr, ~~~~~~~~~~~~~~~ outf, mdebin, ekind, f, ~~~~~~~~~~~~~~~~~~~~~~~ isCheckpointingStep, doRerun, isLastStep, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdrunOptions.writeConfout, ~~~~~~~~~~~~~~~~~~~~~~~~~~ bSumEkinhOld); ~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:53: /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:544:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state, flocal, ftemp); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:554:45: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mimicCommunicator.sendForces(ftemp, state_global->natoms); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:569:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_steep()': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &state->s, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->f); ~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/handlerestart.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/mdmodules.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.h:50, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:46: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp:55: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.h:50, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:46: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = gmx::BasicVector]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp:55: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_tpi()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp:647:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, nullptr, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, &top_global->groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_global->box, state_global->x.arrayRefWithPadding(), &state_global->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_global->lambda, ~~~~~~~~~~~~~~~~~~~~~ nullptr, fr, ppForceWorkload, nullptr, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS : 0) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bStateChanged ? GMX_FORCE_STATECHANGED : 0), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdOpenBalanceRegionBeforeForceComputation::no, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdCloseBalanceRegionAfterForceComputation::no); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp: In member function 'int gmx::Mdrunner::mdrunner()': /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:913:43: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cr->dd = init_domain_decomposition(mdlog, cr, domdecOptions, mdrunOptions, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &mtop, inputrec, ~~~~~~~~~~~~~~~~ box, positionsFromStatePointer(globalState.get()), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &atomSets); ~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:1269:38: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 constructVsitesGlobal(mtop, globalState->x); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractoption.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractsection.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/behaviorcollection.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/options.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsassigner.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsection.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsvisitor.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate::ValueList*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/timeunitmanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/treesupport.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/manager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:60, from /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.h:49, from /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.cpp:38: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr, const std::vector&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/taskassignment.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectory/energyframe.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectory/trajectoryframe.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /build/gromacs-2019.1/src/gromacs/mimic/MimicUtils.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.h:39, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef >, int)': /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void gmx::MimicCommunicator::sendForces(gmx::ArrayRef forces, int natoms) ^~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.h:39, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp:37: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs_d.so.4 -o ../../lib/libgromacs_d.so.4.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp -Wl,-rpath,:::::::::::::::::::::::::::::::::: /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -fopenmp -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.4.0.0 ../../lib/libgromacs_d.so.4 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 98%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f 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-D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../lib/libgromacs_d.so.4.0.0 -fopenmp -lm make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [100%] Built target template make[2]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -j3 -C build/basic tests make[1]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic/CMakeFiles 84 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/external/googletest /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/external/googletest /build/gromacs-2019.1/build/basic/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 0%] Built target mdrun_test_objlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend [ 1%] Built target tng_io_obj /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build Scanning dependencies of target gmock make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googlemock/src/gmock-all.cc [ 4%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 17%] Built target libgromacs_generated /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs /build/gromacs-2019.1/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= [ 17%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 19%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/basic/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googletest/src/gtest-all.cc Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 19%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/datatest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/mock_datamodule.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 19%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 79%] Built target libgromacs cd /build/gromacs-2019.1/build/basic/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/basic/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o /usr/bin/ranlib ../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 79%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/testutils /build/gromacs-2019.1/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 79%] Built target analysisdata-test-shared Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-2019.1/src/testutils/cmdlinetest.cpp cd /build/gromacs-2019.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata-xml.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 80%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make 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/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/testutils/tests /build/gromacs-2019.1/build/basic/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target testutils-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/mpitest.cpp Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/interactivetest.cpp Scanning dependencies of target mdrun-non-integrator-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../lib/libtestutils.a ../../../lib/libgromacs.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/refdata_tests.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 80%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/mdebin.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/rerun.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-non-integrator-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../lib/libtestutils.a ../../../lib/libgromacs.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 82%] Built target mdrun-non-integrator-test /usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 83%] Built target testutils-test cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/simulationsignal.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target applied-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 83%] Built target applied-forces-test /usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target listed-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/tests/bonded.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/commandline/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 83%] Built target listed-forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 84%] Built target mdlib-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/domdec/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/ewald/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/hashedmap.cpp Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 84%] Built target domdec-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fft/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/fft/tests /build/gromacs-2019.1/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 85%] Built target fft-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/pargs.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 86%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/hardware/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests /build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 88%] Built target commandline-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/math/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/math/tests /build/gromacs-2019.1/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 88%] Built target ewald-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/math/arrayrefwithpadding.h:49, from /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp:43: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/math/arrayrefwithpadding.h:49, from /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 88%] Built target hardware-test cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 88%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpmanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp:49: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 88%] Built target mdrunutility-mpi-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/options/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/options/tests /build/gromacs-2019.1/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 88%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/random/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/random/tests /build/gromacs-2019.1/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp In file included from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:59: /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef >, int) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void fillInputContents(ArrayRef < BasicVector < T>> inputRef, ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void compareViews(ArrayRef input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef >, gmx::ArrayRef >) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void compareViews(ArrayRef < BasicVector < T>> input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoption.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector, gmx::Allocator, gmx::AlignedAllocationPolicy> >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector, std::allocator > >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/seed.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/option.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 In file included from /usr/include/c++/8/vector:64, from /usr/include/c++/8/bits/random.h:34, from /usr/include/c++/8/random:49, from /build/gromacs-2019.1/src/gromacs/random/seed.h:51, from /build/gromacs-2019.1/src/gromacs/random/threefry.h:51, from /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 vector(initializer_list __l, ^~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 89%] Built target math-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/restraint/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests /build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 89%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tables/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/tables/tests /build/gromacs-2019.1/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/repeatingsection.cpp Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}}, ^~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 90%] Built target random-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/timeunitmanager.cpp /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}}, ^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 90%] Built target taskassignment-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 90%] Built target table-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend [ 90%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fileio/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 91%] Built target options-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/pulling/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests /build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 91%] Built target pull-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/awh/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/arrayref.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 91%] Built target fileio-test cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.h:57, from /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask64.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 92%] Built target awh-test cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask128.cpp /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/simd/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/base.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/gmxregex.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/path.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/compat/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/make_unique.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 95%] Built target simd-test cd /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 95%] Built target compat-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxana/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxana-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/entropy.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_trjconv.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_msd.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp Scanning dependencies of target pdb2gmx-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 96%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm Scanning dependencies of target gmxpreprocess-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 97%] Built target pdb2gmx-test [ 97%] Built target utility-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= Scanning dependencies of target correlations-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/autocorr.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm Scanning dependencies of target analysisdata-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/analysisdata.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 97%] Built target gmxpreprocess-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/selection/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= Scanning dependencies of target selection-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/indexutil.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/nbsearch.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 97%] Built target correlations-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryanalysis-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/poscalc.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/average.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/selectioncollection.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/histogram.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/analysisdata-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 97%] Built target analysisdata-test cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/selectionoption.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/toputils.cpp /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/energyanalysis/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target energyanalysis-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 97%] Built target energyanalysis-test cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tools/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/trajectoryanalysis-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm Scanning dependencies of target tool-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/report-methods.cpp.o -c /build/gromacs-2019.1/src/gromacs/tools/tests/report-methods.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target trajectoryanalysis-test cd /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/compressed_x_output.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target legacy-mdrun-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/tpitest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/tool-test.dir/report-methods.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/grompp.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/initialconstraints.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/legacy-mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/legacy-mdrun-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target legacy-mdrun-test cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/interactiveMD.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/pmetest.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/swapcoords.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/termination.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/multisim.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/pmetest.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/replicaexchange.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm [100%] Built target mdrun-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target mdrun-mpi-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1 /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/basic' make[1]: Leaving directory '/build/gromacs-2019.1/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/gromacs-2019.1/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 ) UpdateCTestConfiguration from :/build/gromacs-2019.1/build/basic/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-2019.1/build/basic/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/basic/DartConfiguration.tcl Test project /build/gromacs-2019.1/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/gromacs-2019.1/build/basic/bin/testutils-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (80 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (111 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariants 1: [ OK ] ReferenceDataTest.HandlesVariants (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (27 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (40 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (22 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (1 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (1 ms) 1: [----------] 4 tests from XvgTests (25 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (176 ms total) 1: [ PASSED ] 59 tests. 1/40 Test #1: TestUtilsUnitTests ............... Passed 1.36 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /build/gromacs-2019.1/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (45 ms) 2: [----------] 1 test from MpiSelfTest (45 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (45 ms total) 2: [ PASSED ] 1 test. 2/40 Test #2: TestUtilsMpiUnitTests ............ Passed 0.28 sec test 3 Start 3: MdlibUnitTest 3: Test command: /build/gromacs-2019.1/build/basic/bin/mdlib-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdlibUnitTest.xml" 3: Test timeout computed to be: 30 3: [==========] Running 50 tests from 8 test cases. 3: [----------] Global test environment set-up. 3: [----------] 1 test from VerletBufferConstraintTest 3: [ RUN ] VerletBufferConstraintTest.EqualMasses 3: [ OK ] VerletBufferConstraintTest.EqualMasses (38 ms) 3: [----------] 1 test from VerletBufferConstraintTest (38 ms total) 3: 3: [----------] 3 tests from PrintEbin 3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (192 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (26 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (14 ms) 3: [----------] 3 tests from PrintEbin (232 ms total) 3: 3: [----------] 4 tests from ShakeTest 3: [ RUN ] ShakeTest.ConstrainsOneBond 3: [ OK ] ShakeTest.ConstrainsOneBond (15 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (1 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 3: [----------] 4 tests from ShakeTest (16 ms total) 3: 3: [----------] 1 test from NullSignalTest 3: [ RUN ] NullSignalTest.NullSignallerWorks 3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 3: [----------] 1 test from NullSignalTest (0 ms total) 3: 3: [----------] 7 tests from SignalTest 3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 3: [----------] 7 tests from SignalTest (0 ms total) 3: 3: [----------] 9 tests from UpdateGroups 3: [ RUN ] UpdateGroups.ethaneUA 3: [ OK ] UpdateGroups.ethaneUA (58 ms) 3: [ RUN ] UpdateGroups.methane 3: [ OK ] UpdateGroups.methane (0 ms) 3: [ RUN ] UpdateGroups.ethane 3: [ OK ] UpdateGroups.ethane (16 ms) 3: [ RUN ] UpdateGroups.butaneUA 3: [ OK ] UpdateGroups.butaneUA (0 ms) 3: [ RUN ] UpdateGroups.waterThreeSite 3: [ OK ] UpdateGroups.waterThreeSite (0 ms) 3: [ RUN ] UpdateGroups.waterFourSite 3: [ OK ] UpdateGroups.waterFourSite (0 ms) 3: [ RUN ] UpdateGroups.fourAtomsWithSettle 3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 3: [ RUN ] UpdateGroups.waterFlexAngle 3: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 3: [ RUN ] UpdateGroups.twoMoltypes 3: [ OK ] UpdateGroups.twoMoltypes (0 ms) 3: [----------] 9 tests from UpdateGroups (76 ms total) 3: 3: [----------] 1 test from UpdateGroupsCog 3: [ RUN ] UpdateGroupsCog.ComputesCogs 3: [ OK ] UpdateGroupsCog.ComputesCogs (10 ms) 3: [----------] 1 test from UpdateGroupsCog (10 ms total) 3: 3: [----------] 24 tests from WithParameters/SettleTest 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (8 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms) 3: [----------] 24 tests from WithParameters/SettleTest (10 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 50 tests from 8 test cases ran. (382 ms total) 3: [ PASSED ] 50 tests. 3/40 Test #3: MdlibUnitTest .................... Passed 0.66 sec test 4 Start 4: AppliedForcesUnitTest 4: Test command: /build/gromacs-2019.1/build/basic/bin/applied-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 4: Test timeout computed to be: 30 4: [==========] Running 3 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 3 tests from ElectricFieldTest 4: [ RUN ] ElectricFieldTest.Static 4: [ OK ] ElectricFieldTest.Static (56 ms) 4: [ RUN ] ElectricFieldTest.Oscillating 4: [ OK ] ElectricFieldTest.Oscillating (0 ms) 4: [ RUN ] ElectricFieldTest.Pulsed 4: [ OK ] ElectricFieldTest.Pulsed (0 ms) 4: [----------] 3 tests from ElectricFieldTest (56 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 3 tests from 1 test case ran. (56 ms total) 4: [ PASSED ] 3 tests. 4/40 Test #4: AppliedForcesUnitTest ............ Passed 0.39 sec test 5 Start 5: ListedForcesTest 5: Test command: /build/gromacs-2019.1/build/basic/bin/listed-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/ListedForcesTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 15 tests from 1 test case. 5: [----------] Global test environment set-up. 5: [----------] 15 tests from BondedTest 5: [ RUN ] BondedTest.BondAnglePbcNone 5: [ OK ] BondedTest.BondAnglePbcNone (100 ms) 5: [ RUN ] BondedTest.BondAnglePbcXy 5: [ OK ] BondedTest.BondAnglePbcXy (24 ms) 5: [ RUN ] BondedTest.BondAnglePbcXyz 5: [ OK ] BondedTest.BondAnglePbcXyz (25 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcNone 5: [ OK ] BondedTest.DihedralAnglePbcNone (1 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXy 5: [ OK ] BondedTest.DihedralAnglePbcXy (1 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXyz 5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcNo 5: [ OK ] BondedTest.IfuncBondsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXy 5: [ OK ] BondedTest.IfuncBondsPbcXy (1 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXyz 5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcNo 5: [ OK ] BondedTest.IfuncAnglesPbcNo (31 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXy 5: [ OK ] BondedTest.IfuncAnglesPbcXy (45 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ 5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (21 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo 5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (21 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (20 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (22 ms) 5: [----------] 15 tests from BondedTest (312 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 15 tests from 1 test case ran. (313 ms total) 5: [ PASSED ] 15 tests. 5/40 Test #5: ListedForcesTest ................. Passed 0.50 sec test 6 Start 6: CommandLineUnitTests 6: Test command: /build/gromacs-2019.1/build/basic/bin/commandline-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 6: Test timeout computed to be: 30 6: [==========] Running 55 tests from 6 test cases. 6: [----------] Global test environment set-up. 6: [----------] 3 tests from CommandLineHelpModuleTest 6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (274 ms) 6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (43 ms) 6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (31 ms) 6: [----------] 3 tests from CommandLineHelpModuleTest (348 ms total) 6: 6: [----------] 6 tests from CommandLineHelpWriterTest 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (119 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (68 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (60 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms) 6: [----------] 6 tests from CommandLineHelpWriterTest (251 ms total) 6: 6: [----------] 6 tests from CommandLineModuleManagerTest 6: [ RUN ] CommandLineModuleManagerTest.RunsModule 6: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 6: [----------] 6 tests from CommandLineModuleManagerTest (2 ms total) 6: 6: [----------] 13 tests from CommandLineParserTest 6: [ RUN ] CommandLineParserTest.HandlesSingleValues 6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (50 ms) 6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesString 6: [ OK ] CommandLineParserTest.HandlesString (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (62 ms) 6: [----------] 13 tests from CommandLineParserTest (112 ms total) 6: 6: [----------] 6 tests from CommandLineProgramContextTest 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (94 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (66 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (1 ms) 6: [----------] 6 tests from CommandLineProgramContextTest (161 ms total) 6: 6: [----------] 21 tests from ParseCommonArgsTest 6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (34 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (1 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (22 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (32 ms) 6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 6: [----------] 21 tests from ParseCommonArgsTest (92 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 55 tests from 6 test cases ran. (967 ms total) 6: [ PASSED ] 55 tests. 6/40 Test #6: CommandLineUnitTests ............. Passed 1.27 sec test 7 Start 7: DomDecTests 7: Test command: /build/gromacs-2019.1/build/basic/bin/domdec-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/DomDecTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 9 tests from 2 test cases. 7: [----------] Global test environment set-up. 7: [----------] 7 tests from HashedMap 7: [ RUN ] HashedMap.InsertsFinds 7: [ OK ] HashedMap.InsertsFinds (0 ms) 7: [ RUN ] HashedMap.NegativeKeysWork 7: [ OK ] HashedMap.NegativeKeysWork (0 ms) 7: [ RUN ] HashedMap.InsertsErases 7: [ OK ] HashedMap.InsertsErases (0 ms) 7: [ RUN ] HashedMap.InsertsOrAssigns 7: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 7: [ RUN ] HashedMap.Clears 7: [ OK ] HashedMap.Clears (0 ms) 7: [ RUN ] HashedMap.LinkedEntries 7: [ OK ] HashedMap.LinkedEntries (0 ms) 7: [ RUN ] HashedMap.ResizesTable 7: [ OK ] HashedMap.ResizesTable (0 ms) 7: [----------] 7 tests from HashedMap (0 ms total) 7: 7: [----------] 2 tests from LocalAtomSetManager 7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 7: [----------] 2 tests from LocalAtomSetManager (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 9 tests from 2 test cases ran. (0 ms total) 7: [ PASSED ] 9 tests. 7/40 Test #7: DomDecTests ...................... Passed 0.35 sec test 8 Start 8: EwaldUnitTests 8: Test command: /build/gromacs-2019.1/build/basic/bin/ewald-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/EwaldUnitTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 257 tests from 10 test cases. 8: [----------] Global test environment set-up. 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (266 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (267 ms total) 8: 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (144 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (165 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (44 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (56 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (103 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (117 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (45 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (41 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (50 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (27 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (73 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (24 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (33 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (57 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (24 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (21 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (42 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (23 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (50 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (23 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (55 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (34 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (47 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (50 ms) 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (1353 ms total) 8: 8: [----------] 144 tests from SaneInput/PmeGatherTest 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (28 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (33 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (41 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (10 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (38 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (12 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (42 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (36 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (43 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (29 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (24 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (29 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (23 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (50 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (26 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (32 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (42 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (40 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (134 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (99 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (49 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (19 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (47 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (24 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (28 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (36 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (48 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (41 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (26 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (47 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (11 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (36 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (14 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (45 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (70 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (51 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (51 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (36 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (18 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (40 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (42 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (50 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (20 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (27 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (72 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (368 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (350 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (141 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (67 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (104 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (52 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (11 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (80 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (19 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (23 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (122 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (367 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (59 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (51 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (42 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (101 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (84 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (30 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (19 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (37 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (12 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (40 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (27 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (93 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (54 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (10 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (36 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (36 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (44 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (20 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (19 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (53 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (38 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (33 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (23 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (68 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (14 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (15 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (21 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (21 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (26 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (34 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (27 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (29 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (3 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (18 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (2 ms) 8: [----------] 144 tests from SaneInput/PmeGatherTest (5060 ms total) 8: 8: [----------] 16 tests from SaneInput/PmeSolveTest 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (5 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (6 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (37 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (30 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (12 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (24 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (4 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (4 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (39 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (46 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (24 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (26 ms) 8: [----------] 16 tests from SaneInput/PmeSolveTest (269 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (9 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (47 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (9 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (36 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (15 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (33 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (33 ms) 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (184 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (60 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (43 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (49 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (33 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (5 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (4 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (37 ms) 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (235 ms total) 8: 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (26 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (25 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (40 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (41 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (22 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (45 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (57 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (12 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (25 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (27 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (26 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (32 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (32 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (24 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (34 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (26 ms) 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (495 ms total) 8: 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (25 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (40 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (16 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (39 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (11 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (37 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (11 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (8 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (25 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (25 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (7 ms) 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (253 ms total) 8: 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (66 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (33 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (4 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (5 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (9 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (19 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (25 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (18 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (42 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (78 ms) 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (312 ms total) 8: 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (11 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (59 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (64 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (64 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (30 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (67 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (15 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (66 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (46 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (145 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (60 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (67 ms) 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (704 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 257 tests from 10 test cases ran. (9656 ms total) 8: [ PASSED ] 257 tests. 8/40 Test #8: EwaldUnitTests ................... Passed 10.17 sec test 9 Start 9: FFTUnitTests 9: Test command: /build/gromacs-2019.1/build/basic/bin/fft-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/FFTUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 14 tests from 4 test cases. 9: [----------] Global test environment set-up. 9: [----------] 2 tests from ManyFFTTest 9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (148 ms) 9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (77 ms) 9: [----------] 2 tests from ManyFFTTest (226 ms total) 9: 9: [----------] 1 test from FFTTest 9: [ RUN ] FFTTest.Real2DLength18_15Test 9: [ OK ] FFTTest.Real2DLength18_15Test (33 ms) 9: [----------] 1 test from FFTTest (33 ms total) 9: 9: [----------] 1 test from FFFTest3D 9: [ RUN ] FFFTest3D.Real5_6_9 9: [ OK ] FFFTest3D.Real5_6_9 (88 ms) 9: [----------] 1 test from FFFTest3D (89 ms total) 9: 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (45 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (13 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (3 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (51 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (77 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (5 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (97 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (62 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (46 ms) 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (401 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 14 tests from 4 test cases ran. (750 ms total) 9: [ PASSED ] 14 tests. 9/40 Test #9: FFTUnitTests ..................... Passed 1.00 sec test 10 Start 10: GpuUtilsUnitTests 10: Test command: /build/gromacs-2019.1/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 60 tests from 19 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Swap 10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Comparison 10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Swap 10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Comparison 10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Swap 10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Comparison 10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Swap 10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Comparison 10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 10: 10: [----------] 1 test from HostAllocatorUntypedTest 10: [ RUN ] HostAllocatorUntypedTest.Comparison 10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.Move 10: [ OK ] AllocatorTest/0.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/0 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.Move 10: [ OK ] AllocatorTest/1.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/1 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.Move 10: [ OK ] AllocatorTest/2.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/2 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.Move 10: [ OK ] AllocatorTest/3.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/3 (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 60 tests from 19 test cases ran. (3 ms total) 10: [ PASSED ] 60 tests. 10/40 Test #10: GpuUtilsUnitTests ................ Passed 0.22 sec test 11 Start 11: HardwareUnitTests 11: Test command: /build/gromacs-2019.1/build/basic/bin/hardware-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/HardwareUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 4 tests from 1 test case. 11: [----------] Global test environment set-up. 11: [----------] 4 tests from HardwareTopologyTest 11: [ RUN ] HardwareTopologyTest.Execute 11: [ OK ] HardwareTopologyTest.Execute (9 ms) 11: [ RUN ] HardwareTopologyTest.HwlocExecute 11: [ OK ] HardwareTopologyTest.HwlocExecute (8 ms) 11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (8 ms) 11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (8 ms) 11: [----------] 4 tests from HardwareTopologyTest (33 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 4 tests from 1 test case ran. (34 ms total) 11: [ PASSED ] 4 tests. 11/40 Test #11: HardwareUnitTests ................ Passed 0.23 sec test 12 Start 12: MathUnitTests 12: Test command: /build/gromacs-2019.1/build/basic/bin/math-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MathUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 112 tests from 20 test cases. 12: [----------] Global test environment set-up. 12: [----------] 1 test from EmptyArrayRefWithPaddingTest 12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 12: 12: [----------] 6 tests from StructureSimilarityTest 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 12: [----------] 6 tests from StructureSimilarityTest (0 ms total) 12: 12: [----------] 21 tests from FunctionTest 12: [ RUN ] FunctionTest.StaticLog2 12: [ OK ] FunctionTest.StaticLog2 (96 ms) 12: [ RUN ] FunctionTest.Log2I32Bit 12: [ OK ] FunctionTest.Log2I32Bit (13 ms) 12: [ RUN ] FunctionTest.Log2I64Bit 12: [ OK ] FunctionTest.Log2I64Bit (137 ms) 12: [ RUN ] FunctionTest.GreatestCommonDivisor 12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 12: [ RUN ] FunctionTest.InvsqrtFloat 12: [ OK ] FunctionTest.InvsqrtFloat (12 ms) 12: [ RUN ] FunctionTest.InvsqrtDouble 12: [ OK ] FunctionTest.InvsqrtDouble (1 ms) 12: [ RUN ] FunctionTest.InvsqrtInteger 12: [ OK ] FunctionTest.InvsqrtInteger (144 ms) 12: [ RUN ] FunctionTest.InvcbrtFloat 12: [ OK ] FunctionTest.InvcbrtFloat (120 ms) 12: [ RUN ] FunctionTest.InvcbrtDouble 12: [ OK ] FunctionTest.InvcbrtDouble (1 ms) 12: [ RUN ] FunctionTest.InvcbrtInteger 12: [ OK ] FunctionTest.InvcbrtInteger (2 ms) 12: [ RUN ] FunctionTest.SixthrootFloat 12: [ OK ] FunctionTest.SixthrootFloat (77 ms) 12: [ RUN ] FunctionTest.SixthrootDouble 12: [ OK ] FunctionTest.SixthrootDouble (41 ms) 12: [ RUN ] FunctionTest.SixthrootInteger 12: [ OK ] FunctionTest.SixthrootInteger (58 ms) 12: [ RUN ] FunctionTest.InvsixthrootFloat 12: [ OK ] FunctionTest.InvsixthrootFloat (59 ms) 12: [ RUN ] FunctionTest.InvsixthrootDouble 12: [ OK ] FunctionTest.InvsixthrootDouble (24 ms) 12: [ RUN ] FunctionTest.InvsixthrootInteger 12: [ OK ] FunctionTest.InvsixthrootInteger (34 ms) 12: [ RUN ] FunctionTest.Powers 12: [ OK ] FunctionTest.Powers (0 ms) 12: [ RUN ] FunctionTest.ErfInvFloat 12: [ OK ] FunctionTest.ErfInvFloat (22 ms) 12: [ RUN ] FunctionTest.ErfInvDouble 12: [ OK ] FunctionTest.ErfInvDouble (9 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms) 12: [----------] 21 tests from FunctionTest (853 ms total) 12: 12: [----------] 2 tests from InvertMatrixTest 12: [ RUN ] InvertMatrixTest.IdentityIsImpotent 12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertMatrixTest.ComputesInverse 12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 12: [----------] 2 tests from InvertMatrixTest (0 ms total) 12: 12: [----------] 2 tests from InvertBoxMatrixTest 12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanCopyAssign 12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanMoveAssign 12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanSwap 12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanCopyAssign 12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanMoveAssign 12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanSwap 12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanCopyAssign 12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanMoveAssign 12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanSwap 12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanCopyAssign 12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanMoveAssign 12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanSwap 12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/3 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanCopyAssign 12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanMoveAssign 12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanSwap 12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanCopyAssign 12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanMoveAssign 12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanSwap 12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanCopyAssign 12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanMoveAssign 12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanSwap 12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanCopyAssign 12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanMoveAssign 12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanSwap 12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanCopyAssign 12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanMoveAssign 12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanSwap 12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanCopyAssign 12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanMoveAssign 12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanSwap 12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 12: 12: [----------] 33 tests from RVecTest 12: [ RUN ] RVecTest.CanBeStoredInVector 12: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAsMutable_rvec 12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Array 12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 12: [ RUN ] RVecTest.CanAddRVecToRvec 12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanAddAssignRVecToRvec 12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractRVecFromRvec 12: [ OK ] RVecTest.CanSubtractRVecFromRvec (1 ms) 12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanDotProductRVecByRvec 12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanCrossProductRVecByRvec 12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVecInplace 12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 12: [ RUN ] RVecTest.CanScaleRVec 12: [ OK ] RVecTest.CanScaleRVec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVec 12: [ OK ] RVecTest.CanDivideRVec (0 ms) 12: [ RUN ] RVecTest.CanDoUnitvFromRVec 12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanSqLengthOfRVec 12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanLengthOfRVec 12: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToRVec 12: [ OK ] RVecTest.CanCastToRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToDVec 12: [ OK ] RVecTest.CanCastToDVec (0 ms) 12: [ RUN ] RVecTest.CanLeftScalarMultiply 12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanRightScalarMultiply 12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanGetUnitvFromRVec 12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanGetSqLengthOfRVec 12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanGetLengthOfRVec 12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoCrossProductOfRVec 12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoDotProductOfRVec 12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 12: [ RUN ] RVecTest.WorksAs_dvec_Reference 12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_ivec_Reference 12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Reference 12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 12: [ RUN ] RVecTest.CopyConstructorWorks 12: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 12: [ RUN ] RVecTest.CopyAssignmentWorks 12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 12: [ RUN ] RVecTest.MoveConstructorWorks 12: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 12: [ RUN ] RVecTest.MoveAssignmentWorks 12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 12: [----------] 33 tests from RVecTest (1 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 112 tests from 20 test cases ran. (855 ms total) 12: [ PASSED ] 112 tests. 12/40 Test #12: MathUnitTests .................... Passed 1.09 sec test 13 Start 13: MdrunUtilityUnitTests 13: Test command: /build/gromacs-2019.1/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 17 tests from 1 test case. 13: [----------] Global test environment set-up. 13: [----------] 17 tests from ThreadAffinityTest 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 13: NOTE: Affinity setting failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 13: NOTE: Affinity setting for 1/2 threads failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms) 13: [----------] 17 tests from ThreadAffinityTest (9 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 17 tests from 1 test case ran. (9 ms total) 13: [ PASSED ] 17 tests. 13/40 Test #13: MdrunUtilityUnitTests ............ Passed 0.32 sec test 14 Start 14: MdrunUtilityMpiUnitTests 14: Test command: /build/gromacs-2019.1/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 13 tests from 2 test cases. 14: [----------] Global test environment set-up. 14: [----------] 6 tests from ThreadAffinityMultiRankTest 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (14 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (3 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (1 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (1 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (1 ms) 14: [----------] 6 tests from ThreadAffinityMultiRankTest (21 ms total) 14: 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (2 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (15 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (17 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (2 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (2 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (2 ms) 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (42 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 13 tests from 2 test cases ran. (63 ms total) 14: [ PASSED ] 13 tests. 14/40 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.29 sec test 15 Start 15: OnlineHelpUnitTests 15: Test command: /build/gromacs-2019.1/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 22 tests from 4 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from TextTableFormatterTest 15: [ RUN ] TextTableFormatterTest.HandlesBasicCase 15: [ OK ] TextTableFormatterTest.HandlesBasicCase (26 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (24 ms) 15: [ RUN ] TextTableFormatterTest.HandlesIndentation 15: [ OK ] TextTableFormatterTest.HandlesIndentation (16 ms) 15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (8 ms) 15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (24 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 15: [----------] 6 tests from TextTableFormatterTest (100 ms total) 15: 15: [----------] 3 tests from HelpManagerTest 15: [ RUN ] HelpManagerTest.HandlesRootTopic 15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 15: [ RUN ] HelpManagerTest.HandlesSubTopics 15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 15: [ RUN ] HelpManagerTest.HandlesInvalidTopics 15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 15: [----------] 3 tests from HelpManagerTest (1 ms total) 15: 15: [----------] 2 tests from HelpTopicFormattingTest 15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (9 ms) 15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (8 ms) 15: [----------] 2 tests from HelpTopicFormattingTest (17 ms total) 15: 15: [----------] 11 tests from HelpWriterContextTest 15: [ RUN ] HelpWriterContextTest.FormatsParagraphs 15: [ OK ] HelpWriterContextTest.FormatsParagraphs (8 ms) 15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (9 ms) 15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (23 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralText 15: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (34 ms) 15: [ RUN ] HelpWriterContextTest.FormatsBulletList 15: [ OK ] HelpWriterContextTest.FormatsBulletList (9 ms) 15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (15 ms) 15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (10 ms) 15: [ RUN ] HelpWriterContextTest.FormatsGridTable 15: [ OK ] HelpWriterContextTest.FormatsGridTable (8 ms) 15: [ RUN ] HelpWriterContextTest.FormatsTitles 15: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms) 15: [----------] 11 tests from HelpWriterContextTest (119 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 22 tests from 4 test cases ran. (237 ms total) 15: [ PASSED ] 22 tests. 15/40 Test #15: OnlineHelpUnitTests .............. Passed 0.51 sec test 16 Start 16: OptionsUnitTests 16: Test command: /build/gromacs-2019.1/build/basic/bin/options-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/OptionsUnitTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 110 tests from 18 test cases. 16: [----------] Global test environment set-up. 16: [----------] 5 tests from AbstractOptionStorageTest 16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 16: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 16: 16: [----------] 8 tests from FileNameOptionTest 16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (1 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 16: [----------] 8 tests from FileNameOptionTest (1 ms total) 16: 16: [----------] 15 tests from FileNameOptionManagerTest 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 16: 16: [----------] 1 test from OptionsTest 16: [ RUN ] OptionsTest.FailsOnNonsafeStorage 16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 16: [----------] 1 test from OptionsTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerTest 16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMissingValue 16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesExtraValue 16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesGroups 16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesSections 16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 16: [----------] 9 tests from OptionsAssignerTest (2 ms total) 16: 16: [----------] 4 tests from OptionsAssignerBooleanTest 16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 16: 16: [----------] 13 tests from OptionsAssignerIntegerTest 16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 16: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total) 16: 16: [----------] 5 tests from OptionsAssignerDoubleTest 16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 16: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerStringTest 16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 16: 16: [----------] 6 tests from OptionsAssignerEnumTest 16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total) 16: 16: [----------] 8 tests from RepeatingOptionSectionTest 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 16: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 16: 16: [----------] 1 test from TimeUnitManagerTest 16: [ RUN ] TimeUnitManagerTest.BasicOperations 16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 16: [----------] 1 test from TimeUnitManagerTest (0 ms total) 16: 16: [----------] 4 tests from TimeUnitBehaviorTest 16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 16: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 16: 16: [----------] 2 tests from TreeValueSupportAssignTest 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 16: [----------] 2 tests from TreeValueSupportAssignTest (2 ms total) 16: 16: [----------] 1 test from TreeValueSupportAssignErrorTest 16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 16: 16: [----------] 5 tests from TreeValueSupportCheckTest 16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 16: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 16: 16: [----------] 6 tests from TreeValueSupportAdjustTest 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (101 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (25 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (26 ms) 16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (14 ms) 16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (18 ms) 16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (25 ms) 16: [----------] 6 tests from TreeValueSupportAdjustTest (209 ms total) 16: 16: [----------] 8 tests from TreeValueSupportTest 16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (12 ms) 16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (21 ms) 16: [ RUN ] TreeValueSupportTest.SupportsInt64Option 16: [ OK ] TreeValueSupportTest.SupportsInt64Option (27 ms) 16: [ RUN ] TreeValueSupportTest.SupportsStringOption 16: [ OK ] TreeValueSupportTest.SupportsStringOption (15 ms) 16: [ RUN ] TreeValueSupportTest.SupportsFloatOption 16: [ OK ] TreeValueSupportTest.SupportsFloatOption (8 ms) 16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (8 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (9 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumOption 16: [ OK ] TreeValueSupportTest.SupportsEnumOption (16 ms) 16: [----------] 8 tests from TreeValueSupportTest (116 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 110 tests from 18 test cases ran. (334 ms total) 16: [ PASSED ] 110 tests. 16/40 Test #16: OptionsUnitTests ................. Passed 0.61 sec test 17 Start 17: RandomUnitTests 17: Test command: /build/gromacs-2019.1/build/basic/bin/random-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/RandomUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 44 tests from 10 test cases. 17: [----------] Global test environment set-up. 17: [----------] 4 tests from ExponentialDistributionTest 17: [ RUN ] ExponentialDistributionTest.Output 17: [ OK ] ExponentialDistributionTest.Output (56 ms) 17: [ RUN ] ExponentialDistributionTest.Logical 17: [ OK ] ExponentialDistributionTest.Logical (0 ms) 17: [ RUN ] ExponentialDistributionTest.Reset 17: [ OK ] ExponentialDistributionTest.Reset (0 ms) 17: [ RUN ] ExponentialDistributionTest.AltParam 17: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from ExponentialDistributionTest (56 ms total) 17: 17: [----------] 4 tests from GammaDistributionTest 17: [ RUN ] GammaDistributionTest.Output 17: [ OK ] GammaDistributionTest.Output (25 ms) 17: [ RUN ] GammaDistributionTest.Logical 17: [ OK ] GammaDistributionTest.Logical (0 ms) 17: [ RUN ] GammaDistributionTest.Reset 17: [ OK ] GammaDistributionTest.Reset (0 ms) 17: [ RUN ] GammaDistributionTest.AltParam 17: [ OK ] GammaDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from GammaDistributionTest (25 ms total) 17: 17: [----------] 4 tests from NormalDistributionTest 17: [ RUN ] NormalDistributionTest.Output 17: [ OK ] NormalDistributionTest.Output (33 ms) 17: [ RUN ] NormalDistributionTest.Logical 17: [ OK ] NormalDistributionTest.Logical (0 ms) 17: [ RUN ] NormalDistributionTest.Reset 17: [ OK ] NormalDistributionTest.Reset (0 ms) 17: [ RUN ] NormalDistributionTest.AltParam 17: [ OK ] NormalDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from NormalDistributionTest (33 ms total) 17: 17: [----------] 1 test from SeedTest 17: [ RUN ] SeedTest.makeRandomSeed 17: [ OK ] SeedTest.makeRandomSeed (0 ms) 17: [----------] 1 test from SeedTest (0 ms total) 17: 17: [----------] 6 tests from TabulatedNormalDistributionTest 17: [ RUN ] TabulatedNormalDistributionTest.Output14 17: [ OK ] TabulatedNormalDistributionTest.Output14 (41 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Output16 17: [ OK ] TabulatedNormalDistributionTest.Output16 (14 ms) 17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (1 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Logical 17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Reset 17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.AltParam 17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 17: [----------] 6 tests from TabulatedNormalDistributionTest (57 ms total) 17: 17: [----------] 1 test from TabulatedNormalDistributionTableTest 17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (5 ms) 17: [----------] 1 test from TabulatedNormalDistributionTableTest (5 ms total) 17: 17: [----------] 6 tests from ThreeFry2x64Test 17: [ RUN ] ThreeFry2x64Test.Logical 17: [ OK ] ThreeFry2x64Test.Logical (0 ms) 17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (10 ms) 17: [ RUN ] ThreeFry2x64Test.Reseed 17: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 17: [ RUN ] ThreeFry2x64Test.Discard 17: [ OK ] ThreeFry2x64Test.Discard (0 ms) 17: [ RUN ] ThreeFry2x64Test.InvalidCounter 17: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 17: [----------] 6 tests from ThreeFry2x64Test (10 ms total) 17: 17: [----------] 4 tests from UniformIntDistributionTest 17: [ RUN ] UniformIntDistributionTest.Output 17: [ OK ] UniformIntDistributionTest.Output (8 ms) 17: [ RUN ] UniformIntDistributionTest.Logical 17: [ OK ] UniformIntDistributionTest.Logical (0 ms) 17: [ RUN ] UniformIntDistributionTest.Reset 17: [ OK ] UniformIntDistributionTest.Reset (0 ms) 17: [ RUN ] UniformIntDistributionTest.AltParam 17: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from UniformIntDistributionTest (9 ms total) 17: 17: [----------] 5 tests from UniformRealDistributionTest 17: [ RUN ] UniformRealDistributionTest.GenerateCanonical 17: [ OK ] UniformRealDistributionTest.GenerateCanonical (8 ms) 17: [ RUN ] UniformRealDistributionTest.Output 17: [ OK ] UniformRealDistributionTest.Output (9 ms) 17: [ RUN ] UniformRealDistributionTest.Logical 17: [ OK ] UniformRealDistributionTest.Logical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Reset 17: [ OK ] UniformRealDistributionTest.Reset (0 ms) 17: [ RUN ] UniformRealDistributionTest.AltParam 17: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 17: [----------] 5 tests from UniformRealDistributionTest (17 ms total) 17: 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (23 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (9 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (9 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (8 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (51 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 44 tests from 10 test cases ran. (263 ms total) 17: [ PASSED ] 44 tests. 17/40 Test #17: RandomUnitTests .................. Passed 0.58 sec test 18 Start 18: RestraintTests 18: Test command: /build/gromacs-2019.1/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/RestraintTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 1 test from 1 test case. 18: [----------] Global test environment set-up. 18: [----------] 1 test from RestraintManager 18: [ RUN ] RestraintManager.restraintList 18: [ OK ] RestraintManager.restraintList (1 ms) 18: [----------] 1 test from RestraintManager (1 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1 test from 1 test case ran. (1 ms total) 18: [ PASSED ] 1 test. 18/40 Test #18: RestraintTests ................... Passed 0.16 sec test 19 Start 19: TableUnitTests 19: Test command: /build/gromacs-2019.1/build/basic/bin/table-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/TableUnitTests.xml" 19: Test timeout computed to be: 30 19: [==========] Running 16 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (5 ms) 19: [ RUN ] SplineTableTest/0.Sinc 19: [ OK ] SplineTableTest/0.Sinc (2 ms) 19: [ RUN ] SplineTableTest/0.LJ12 19: [ OK ] SplineTableTest/0.LJ12 (63 ms) 19: [ RUN ] SplineTableTest/0.PmeCorrection 19: [ OK ] SplineTableTest/0.PmeCorrection (4 ms) 19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (2 ms) 19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (3 ms) 19: [ RUN ] SplineTableTest/0.TwoFunctions 19: [ OK ] SplineTableTest/0.TwoFunctions (124 ms) 19: [ RUN ] SplineTableTest/0.ThreeFunctions 19: [ OK ] SplineTableTest/0.ThreeFunctions (135 ms) 19: [----------] 8 tests from SplineTableTest/0 (338 ms total) 19: 19: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (6 ms) 19: [ RUN ] SplineTableTest/1.Sinc 19: [ OK ] SplineTableTest/1.Sinc (2 ms) 19: [ RUN ] SplineTableTest/1.LJ12 19: [ OK ] SplineTableTest/1.LJ12 (10 ms) 19: [ RUN ] SplineTableTest/1.PmeCorrection 19: [ OK ] SplineTableTest/1.PmeCorrection (5 ms) 19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (3 ms) 19: [ RUN ] SplineTableTest/1.TwoFunctions 19: [ OK ] SplineTableTest/1.TwoFunctions (20 ms) 19: [ RUN ] SplineTableTest/1.ThreeFunctions 19: [ OK ] SplineTableTest/1.ThreeFunctions (20 ms) 19: [----------] 8 tests from SplineTableTest/1 (67 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 16 tests from 2 test cases ran. (406 ms total) 19: [ PASSED ] 16 tests. 19/40 Test #19: TableUnitTests ................... Passed 0.56 sec test 20 Start 20: TaskAssignmentUnitTests 20: Test command: /build/gromacs-2019.1/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 3 tests from 1 test case. 20: [----------] Global test environment set-up. 20: [----------] 3 tests from GpuIdStringHandlingTest 20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork 20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (1 ms) 20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid 20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow 20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (0 ms) 20: [----------] 3 tests from GpuIdStringHandlingTest (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 3 tests from 1 test case ran. (1 ms total) 20: [ PASSED ] 3 tests. 20/40 Test #20: TaskAssignmentUnitTests .......... Passed 0.23 sec test 21 Start 21: UtilityUnitTests 21: Test command: /build/gromacs-2019.1/build/basic/bin/utility-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/UtilityUnitTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 325 tests from 52 test cases. 21: [----------] Global test environment set-up. 21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.Move 21: [ OK ] AllocatorTest/0.Move (0 ms) 21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/0 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.Move 21: [ OK ] AllocatorTest/1.Move (0 ms) 21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/1 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.Move 21: [ OK ] AllocatorTest/2.Move (0 ms) 21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/2 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.Move 21: [ OK ] AllocatorTest/3.Move (0 ms) 21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/3 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.Move 21: [ OK ] AllocatorTest/4.Move (0 ms) 21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/4 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.Move 21: [ OK ] AllocatorTest/5.Move (0 ms) 21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/5 (1 ms total) 21: 21: [----------] 1 test from AllocatorUntypedTest 21: [ RUN ] AllocatorUntypedTest.Comparison 21: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 21: [----------] 1 test from AllocatorUntypedTest (0 ms total) 21: 21: [----------] 1 test from EmptyArrayRefTest 21: [ RUN ] EmptyArrayRefTest.IsEmpty 21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyArrayRefTest (0 ms total) 21: 21: [----------] 1 test from EmptyConstArrayRefTest 21: [ RUN ] EmptyConstArrayRefTest.IsEmpty 21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/3 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/14 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 21: 21: [----------] 4 tests from KeyValueTreeSerializerTest 21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (217 ms) 21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (83 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (66 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (67 ms) 21: [----------] 4 tests from KeyValueTreeSerializerTest (434 ms total) 21: 21: [----------] 6 tests from TreeValueTransformTest 21: [ RUN ] TreeValueTransformTest.SimpleTransforms 21: [ OK ] TreeValueTransformTest.SimpleTransforms (56 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (11 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (50 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromString 21: [ OK ] TreeValueTransformTest.ObjectFromString (75 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (51 ms) 21: [ RUN ] TreeValueTransformTest.ScopedTransformRules 21: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 21: [----------] 6 tests from TreeValueTransformTest (243 ms total) 21: 21: [----------] 1 test from TreeValueTransformErrorTest 21: [ RUN ] TreeValueTransformErrorTest.ConversionError 21: [ OK ] TreeValueTransformErrorTest.ConversionError (58 ms) 21: [----------] 1 test from TreeValueTransformErrorTest (58 ms total) 21: 21: [----------] 2 tests from RegexBasicTest 21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported 21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (1 ms) 21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported 21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (0 ms) 21: [----------] 2 tests from RegexBasicTest (2 ms total) 21: 21: [----------] 5 tests from LoggerTest 21: [ RUN ] LoggerTest.EmptyLoggerWorks 21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToStream 21: [ OK ] LoggerTest.LogsToStream (0 ms) 21: [ RUN ] LoggerTest.LogsToFile 21: [ OK ] LoggerTest.LogsToFile (49 ms) 21: [ RUN ] LoggerTest.LevelFilteringWorks 21: [ OK ] LoggerTest.LevelFilteringWorks (56 ms) 21: [ RUN ] LoggerTest.LogsToMultipleStreams 21: [ OK ] LoggerTest.LogsToMultipleStreams (66 ms) 21: [----------] 5 tests from LoggerTest (171 ms total) 21: 21: [----------] 4 tests from MutexBasicTest 21: [ RUN ] MutexBasicTest.CanBeMade 21: [ OK ] MutexBasicTest.CanBeMade (0 ms) 21: [ RUN ] MutexBasicTest.CanBeLocked 21: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeTryLocked 21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 21: [----------] 4 tests from MutexBasicTest (0 ms total) 21: 21: [----------] 3 tests from MutexTaskTest 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 21: [----------] 3 tests from MutexTaskTest (0 ms total) 21: 21: [----------] 4 tests from PathTest 21: [ RUN ] PathTest.StripSourcePrefixWorks 21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks 21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathWorks 21: [ OK ] PathTest.GetParentPathWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathAndBasenameWorks 21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms) 21: [----------] 4 tests from PathTest (1 ms total) 21: 21: [----------] 2 tests from PhysicalNodeCommunicatorTest 21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 21: 21: [----------] 7 tests from StringUtilityTest 21: [ RUN ] StringUtilityTest.StartsWith 21: [ OK ] StringUtilityTest.StartsWith (0 ms) 21: [ RUN ] StringUtilityTest.EndsWith 21: [ OK ] StringUtilityTest.EndsWith (0 ms) 21: [ RUN ] StringUtilityTest.StripSuffixIfPresent 21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 21: [ RUN ] StringUtilityTest.StripString 21: [ OK ] StringUtilityTest.StripString (0 ms) 21: [ RUN ] StringUtilityTest.SplitString 21: [ OK ] StringUtilityTest.SplitString (0 ms) 21: [ RUN ] StringUtilityTest.SplitDelimitedString 21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms) 21: [----------] 7 tests from StringUtilityTest (1 ms total) 21: 21: [----------] 2 tests from FormatStringTest 21: [ RUN ] FormatStringTest.HandlesBasicFormatting 21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 21: [ RUN ] FormatStringTest.HandlesLongStrings 21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 21: [----------] 2 tests from FormatStringTest (0 ms total) 21: 21: [----------] 1 test from StringFormatterTest 21: [ RUN ] StringFormatterTest.HandlesBasicFormatting 21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 21: [----------] 1 test from StringFormatterTest (0 ms total) 21: 21: [----------] 1 test from formatAndJoinTest 21: [ RUN ] formatAndJoinTest.Works 21: [ OK ] formatAndJoinTest.Works (0 ms) 21: [----------] 1 test from formatAndJoinTest (0 ms total) 21: 21: [----------] 1 test from JoinStringsTest 21: [ RUN ] JoinStringsTest.Works 21: [ OK ] JoinStringsTest.Works (0 ms) 21: [----------] 1 test from JoinStringsTest (0 ms total) 21: 21: [----------] 6 tests from ReplaceAllTest 21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesNoMatches 21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 21: [----------] 6 tests from ReplaceAllTest (0 ms total) 21: 21: [----------] 10 tests from TextLineWrapperTest 21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectly 21: [ OK ] TextLineWrapperTest.WrapsCorrectly (26 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (8 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndent 21: [ OK ] TextLineWrapperTest.HandlesIndent (9 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (26 ms) 21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (121 ms) 21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (32 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (13 ms) 21: [----------] 10 tests from TextLineWrapperTest (235 ms total) 21: 21: [----------] 6 tests from TextWriterTest 21: [ RUN ] TextWriterTest.WritesLines 21: [ OK ] TextWriterTest.WritesLines (44 ms) 21: [ RUN ] TextWriterTest.WritesLinesInParts 21: [ OK ] TextWriterTest.WritesLinesInParts (62 ms) 21: [ RUN ] TextWriterTest.WritesWrappedLines 21: [ OK ] TextWriterTest.WritesWrappedLines (39 ms) 21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (22 ms) 21: [ RUN ] TextWriterTest.TracksNewlines 21: [ OK ] TextWriterTest.TracksNewlines (1 ms) 21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (8 ms) 21: [----------] 6 tests from TextWriterTest (176 ms total) 21: 21: [----------] 1 test from TypeTraitsTest 21: [ RUN ] TypeTraitsTest.IsIntegralConstant 21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 21: [----------] 1 test from TypeTraitsTest (0 ms total) 21: 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total) 21: 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 21: 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total) 21: 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (1 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 325 tests from 52 test cases ran. (1330 ms total) 21: [ PASSED ] 325 tests. 21/40 Test #21: UtilityUnitTests ................. Passed 1.78 sec test 22 Start 22: UtilityMpiUnitTests 22: Test command: /build/gromacs-2019.1/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 2 tests from 1 test case. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from PhysicalNodeCommunicatorTest 22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms) 22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (5 ms) 22: [----------] 2 tests from PhysicalNodeCommunicatorTest (6 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test case ran. (7 ms total) 22: [ PASSED ] 2 tests. 22/40 Test #22: UtilityMpiUnitTests .............. Passed 0.17 sec test 23 Start 23: FileIOTests 23: Test command: /build/gromacs-2019.1/build/basic/bin/fileio-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/FileIOTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 17 tests from 4 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from FileMD5Test 23: [ RUN ] FileMD5Test.CanComputeMD5 23: [ OK ] FileMD5Test.CanComputeMD5 (32 ms) 23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms) 23: [----------] 2 tests from FileMD5Test (65 ms total) 23: 23: [----------] 9 tests from ReadTest 23: [ RUN ] ReadTest.get_eint_ReadsInteger 23: [ OK ] ReadTest.get_eint_ReadsInteger (72 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_eint64_ReadsInteger 23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsInteger 23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsFloat 23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 23: [ RUN ] ReadTest.get_ereal_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not a 23: real value 23: 23: 23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 23: [----------] 9 tests from ReadTest (72 ms total) 23: 23: [----------] 2 tests from TngTest 23: [ RUN ] TngTest.CanOpenTngFile 23: [ OK ] TngTest.CanOpenTngFile (66 ms) 23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 23: [----------] 2 tests from TngTest (66 ms total) 23: 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (22 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (97 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (121 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 17 tests from 4 test cases ran. (324 ms total) 23: [ PASSED ] 17 tests. 23/40 Test #23: FileIOTests ...................... Passed 0.47 sec test 24 Start 24: PullTest 24: Test command: /build/gromacs-2019.1/build/basic/bin/pull-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/PullTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 5 tests from 1 test case. 24: [----------] Global test environment set-up. 24: [----------] 5 tests from PullTest 24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (30 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 24: [----------] 5 tests from PullTest (30 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 5 tests from 1 test case ran. (30 ms total) 24: [ PASSED ] 5 tests. 24/40 Test #24: PullTest ......................... Passed 0.23 sec test 25 Start 25: AwhTest 25: Test command: /build/gromacs-2019.1/build/basic/bin/awh-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/AwhTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 12 tests from 4 test cases. 25: [----------] Global test environment set-up. 25: [----------] 1 test from BiasTest 25: [ RUN ] BiasTest.DetectsCovering 25: [ OK ] BiasTest.DetectsCovering (2 ms) 25: [----------] 1 test from BiasTest (2 ms total) 25: 25: [----------] 1 test from gridTest 25: [ RUN ] gridTest.neighborhood 25: [ OK ] gridTest.neighborhood (3 ms) 25: [----------] 1 test from gridTest (3 ms total) 25: 25: [----------] 8 tests from WithParameters/BiasTest 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (84 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (25 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (25 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (23 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (13 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (8 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (9 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (13 ms) 25: [----------] 8 tests from WithParameters/BiasTest (200 ms total) 25: 25: [----------] 2 tests from WithParameters/BiasStateTest 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (32 ms) 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (29 ms) 25: [----------] 2 tests from WithParameters/BiasStateTest (61 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test cases ran. (268 ms total) 25: [ PASSED ] 12 tests. 25/40 Test #25: AwhTest .......................... Passed 0.43 sec test 26 Start 26: SimdUnitTests 26: Test command: /build/gromacs-2019.1/build/basic/bin/simd-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/SimdUnitTests.xml" 26: Test timeout computed to be: 30 26: [==========] Running 86 tests from 3 test cases. 26: [----------] Global test environment set-up. 26: [----------] 41 tests from SimdScalarTest 26: [ RUN ] SimdScalarTest.load 26: [ OK ] SimdScalarTest.load (0 ms) 26: [ RUN ] SimdScalarTest.loadU 26: [ OK ] SimdScalarTest.loadU (0 ms) 26: [ RUN ] SimdScalarTest.store 26: [ OK ] SimdScalarTest.store (0 ms) 26: [ RUN ] SimdScalarTest.storeU 26: [ OK ] SimdScalarTest.storeU (0 ms) 26: [ RUN ] SimdScalarTest.setZero 26: [ OK ] SimdScalarTest.setZero (0 ms) 26: [ RUN ] SimdScalarTest.andNot 26: [ OK ] SimdScalarTest.andNot (0 ms) 26: [ RUN ] SimdScalarTest.fma 26: [ OK ] SimdScalarTest.fma (0 ms) 26: [ RUN ] SimdScalarTest.fms 26: [ OK ] SimdScalarTest.fms (0 ms) 26: [ RUN ] SimdScalarTest.fnma 26: [ OK ] SimdScalarTest.fnma (0 ms) 26: [ RUN ] SimdScalarTest.fnms 26: [ OK ] SimdScalarTest.fnms (0 ms) 26: [ RUN ] SimdScalarTest.maskAdd 26: [ OK ] SimdScalarTest.maskAdd (0 ms) 26: [ RUN ] SimdScalarTest.maskzMul 26: [ OK ] SimdScalarTest.maskzMul (0 ms) 26: [ RUN ] SimdScalarTest.maskzFma 26: [ OK ] SimdScalarTest.maskzFma (0 ms) 26: [ RUN ] SimdScalarTest.abs 26: [ OK ] SimdScalarTest.abs (0 ms) 26: [ RUN ] SimdScalarTest.max 26: [ OK ] SimdScalarTest.max (0 ms) 26: [ RUN ] SimdScalarTest.min 26: [ OK ] SimdScalarTest.min (0 ms) 26: [ RUN ] SimdScalarTest.round 26: [ OK ] SimdScalarTest.round (0 ms) 26: [ RUN ] SimdScalarTest.trunc 26: [ OK ] SimdScalarTest.trunc (0 ms) 26: [ RUN ] SimdScalarTest.reduce 26: [ OK ] SimdScalarTest.reduce (0 ms) 26: [ RUN ] SimdScalarTest.testBits 26: [ OK ] SimdScalarTest.testBits (0 ms) 26: [ RUN ] SimdScalarTest.anyTrue 26: [ OK ] SimdScalarTest.anyTrue (0 ms) 26: [ RUN ] SimdScalarTest.selectByMask 26: [ OK ] SimdScalarTest.selectByMask (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMask 26: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 26: [ RUN ] SimdScalarTest.blend 26: [ OK ] SimdScalarTest.blend (0 ms) 26: [ RUN ] SimdScalarTest.cvtR2I 26: [ OK ] SimdScalarTest.cvtR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvttR2I 26: [ OK ] SimdScalarTest.cvttR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvtI2R 26: [ OK ] SimdScalarTest.cvtI2R (0 ms) 26: [ RUN ] SimdScalarTest.cvtF2D 26: [ OK ] SimdScalarTest.cvtF2D (0 ms) 26: [ RUN ] SimdScalarTest.cvtD2D 26: [ OK ] SimdScalarTest.cvtD2D (0 ms) 26: [ RUN ] SimdScalarTest.loadI 26: [ OK ] SimdScalarTest.loadI (0 ms) 26: [ RUN ] SimdScalarTest.loadUI 26: [ OK ] SimdScalarTest.loadUI (0 ms) 26: [ RUN ] SimdScalarTest.storeI 26: [ OK ] SimdScalarTest.storeI (0 ms) 26: [ RUN ] SimdScalarTest.storeUI 26: [ OK ] SimdScalarTest.storeUI (0 ms) 26: [ RUN ] SimdScalarTest.andNotI 26: [ OK ] SimdScalarTest.andNotI (0 ms) 26: [ RUN ] SimdScalarTest.testBitsI 26: [ OK ] SimdScalarTest.testBitsI (0 ms) 26: [ RUN ] SimdScalarTest.selectByMaskI 26: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMaskI 26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 26: [ RUN ] SimdScalarTest.blendI 26: [ OK ] SimdScalarTest.blendI (0 ms) 26: [ RUN ] SimdScalarTest.cvtB2IB 26: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 26: [ RUN ] SimdScalarTest.cvtIB2B 26: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 26: [ RUN ] SimdScalarTest.expandScalarsToTriplets 26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 26: [----------] 41 tests from SimdScalarTest (1 ms total) 26: 26: [----------] 8 tests from SimdScalarUtilTest 26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 26: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 26: 26: [----------] 37 tests from SimdScalarMathTest 26: [ RUN ] SimdScalarMathTest.copysign 26: [ OK ] SimdScalarMathTest.copysign (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPair 26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 26: [ RUN ] SimdScalarMathTest.inv 26: [ OK ] SimdScalarMathTest.inv (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrt 26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdScalarMathTest.log 26: [ OK ] SimdScalarMathTest.log (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2 26: [ OK ] SimdScalarMathTest.exp2 (0 ms) 26: [ RUN ] SimdScalarMathTest.exp 26: [ OK ] SimdScalarMathTest.exp (0 ms) 26: [ RUN ] SimdScalarMathTest.erf 26: [ OK ] SimdScalarMathTest.erf (0 ms) 26: [ RUN ] SimdScalarMathTest.erfc 26: [ OK ] SimdScalarMathTest.erfc (0 ms) 26: [ RUN ] SimdScalarMathTest.sincos 26: [ OK ] SimdScalarMathTest.sincos (0 ms) 26: [ RUN ] SimdScalarMathTest.sin 26: [ OK ] SimdScalarMathTest.sin (0 ms) 26: [ RUN ] SimdScalarMathTest.cos 26: [ OK ] SimdScalarMathTest.cos (0 ms) 26: [ RUN ] SimdScalarMathTest.tan 26: [ OK ] SimdScalarMathTest.tan (0 ms) 26: [ RUN ] SimdScalarMathTest.asin 26: [ OK ] SimdScalarMathTest.asin (0 ms) 26: [ RUN ] SimdScalarMathTest.acos 26: [ OK ] SimdScalarMathTest.acos (0 ms) 26: [ RUN ] SimdScalarMathTest.atan 26: [ OK ] SimdScalarMathTest.atan (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2 26: [ OK ] SimdScalarMathTest.atan2 (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrection 26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.invSingleAccuracy 26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.logSingleAccuracy 26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.expSingleAccuracy 26: [ OK ] SimdScalarMathTest.expSingleAccuracy (1 ms) 26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 26: [----------] 37 tests from SimdScalarMathTest (1 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 86 tests from 3 test cases ran. (2 ms total) 26: [ PASSED ] 86 tests. 26/40 Test #26: SimdUnitTests .................... Passed 0.21 sec test 27 Start 27: CompatibilityHelpersTests 27: Test command: /build/gromacs-2019.1/build/basic/bin/compat-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 6 tests from 6 test cases. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CompatibilityHelper 27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles 27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms) 27: [----------] 1 test from CompatibilityHelper (0 ms total) 27: 27: [----------] 1 test from NotNullConstruction 27: [ RUN ] NotNullConstruction.Works 27: [ OK ] NotNullConstruction.Works (0 ms) 27: [----------] 1 test from NotNullConstruction (0 ms total) 27: 27: [----------] 1 test from NotNullCasting 27: [ RUN ] NotNullCasting.Works 27: [ OK ] NotNullCasting.Works (0 ms) 27: [----------] 1 test from NotNullCasting (0 ms total) 27: 27: [----------] 1 test from NotNullAssignment 27: [ RUN ] NotNullAssignment.Works 27: [ OK ] NotNullAssignment.Works (0 ms) 27: [----------] 1 test from NotNullAssignment (0 ms total) 27: 27: [----------] 1 test from MakeNotNull 27: [ RUN ] MakeNotNull.Works 27: [ OK ] MakeNotNull.Works (0 ms) 27: [----------] 1 test from MakeNotNull (0 ms total) 27: 27: [----------] 1 test from NotNull 27: [ RUN ] NotNull.WorksInContainers 27: [ OK ] NotNull.WorksInContainers (0 ms) 27: [----------] 1 test from NotNull (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 6 tests from 6 test cases ran. (0 ms total) 27: [ PASSED ] 6 tests. 27/40 Test #27: CompatibilityHelpersTests ........ Passed 0.19 sec test 28 Start 28: GmxAnaTest 28: Test command: /build/gromacs-2019.1/build/basic/bin/gmxana-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/GmxAnaTest.xml" 28: Test timeout computed to be: 600 28: [==========] Running 26 tests from 5 test cases. 28: [----------] Global test environment set-up. 28: [----------] 5 tests from Entropy 28: [ RUN ] Entropy.Schlitter_300_NoLinear 28: [ OK ] Entropy.Schlitter_300_NoLinear (129 ms) 28: [ RUN ] Entropy.Schlitter_300_Linear 28: [ OK ] Entropy.Schlitter_300_Linear (33 ms) 28: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 28: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (14 ms) 28: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 28: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (11 ms) 28: [ RUN ] Entropy.QuasiHarmonic_200_Linear 28: [ OK ] Entropy.QuasiHarmonic_200_Linear (16 ms) 28: [----------] 5 tests from Entropy (203 ms total) 28: 28: [----------] 3 tests from MsdTest 28: [ RUN ] MsdTest.threeDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.threeDimensionalDiffusion (163 ms) 28: [ RUN ] MsdTest.twoDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.twoDimensionalDiffusion (31 ms) 28: [ RUN ] MsdTest.oneDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.oneDimensionalDiffusion (9 ms) 28: [----------] 3 tests from MsdTest (203 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: trr version: GMX_trn_file (single precision) 28: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (44 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (75 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (14 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (25 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (9 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (24 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (191 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (722 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (7 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (6 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (7 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm) 28: -> frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (8 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (7 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (759 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm) 28: -> frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (1 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (8 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 26 tests from 5 test cases ran. (1364 ms total) 28: [ PASSED ] 26 tests. 28/40 Test #28: GmxAnaTest ....................... Passed 1.46 sec test 29 Start 29: GmxPreprocessTests 29: Test command: /build/gromacs-2019.1/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 29: Test timeout computed to be: 30 29: [==========] Running 26 tests from 4 test cases. 29: [----------] Global test environment set-up. 29: [----------] 4 tests from GenconfTest 29: [ RUN ] GenconfTest.nbox_Works 29: [ OK ] GenconfTest.nbox_Works (113 ms) 29: [ RUN ] GenconfTest.nbox_norenumber_Works 29: [ OK ] GenconfTest.nbox_norenumber_Works (32 ms) 29: [ RUN ] GenconfTest.nbox_dist_Works 29: [ OK ] GenconfTest.nbox_dist_Works (19 ms) 29: [ RUN ] GenconfTest.nbox_rot_Works 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: [ OK ] GenconfTest.nbox_rot_Works (18 ms) 29: [----------] 4 tests from GenconfTest (182 ms total) 29: 29: [----------] 5 tests from InsertMoleculesTest 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 8 atoms)! 29: 29: Added 1 molecules (out of 1 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 29: 29: Output configuration contains 8 atoms in 4 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (216 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 2 atoms)! 29: Try 2 success (now 4 atoms)! 29: Try 3 success (now 6 atoms)! 29: Try 4 success (now 8 atoms)! 29: Try 5 success (now 10 atoms)! 29: 29: Added 5 molecules (out of 5 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 29: 29: Output configuration contains 10 atoms in 10 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (47 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 8 atoms)! 29: Try 2 success (now 10 atoms)! 29: 29: Added 2 molecules (out of 2 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 29: 29: Output configuration contains 10 atoms in 4 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (72 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 650 atoms)! 29: Try 2 success (now 652 atoms)! 29: Try 3 success (now 654 atoms)! 29: Try 4 success (now 656 atoms)! 29: 29: Added 4 molecules (out of 4 requested) 29: Replaced 8 residues (24 atoms) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 29: 29: Output configuration contains 632 atoms in 212 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (71 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Read 4 positions from file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 29: 29: Try 1 success (now 2 atoms)! 29: Try 2 success (now 4 atoms)! 29: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 29: Try 13 success (now 6 atoms)! 29: 29: Added 3 molecules (out of 4 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 29: 29: Output configuration contains 6 atoms in 3 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (85 ms) 29: [----------] 5 tests from InsertMoleculesTest (491 ms total) 29: 29: [----------] 12 tests from GetIrTest 29: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp, line 12]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: Ignoring obsolete mdp entry 'title' 29: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 29: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (52 ms) 29: [ RUN ] GetIrTest.HandlesOnlyCutoffScheme 29: [ OK ] GetIrTest.HandlesOnlyCutoffScheme (22 ms) 29: [ RUN ] GetIrTest.UserErrorsSilentlyTolerated 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp, line 5]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.UserErrorsSilentlyTolerated (27 ms) 29: [ RUN ] GetIrTest.DefineHandlesAssignmentOnRhs 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.DefineHandlesAssignmentOnRhs (67 ms) 29: [ RUN ] GetIrTest.EmptyInputWorks 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp, line 1]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.EmptyInputWorks (21 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricField 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricField (34 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldPulsed 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldPulsed (26 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldOscillating 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldOscillating (68 ms) 29: [ RUN ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys 29: [ OK ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys (3 ms) 29: [ RUN ] GetIrTest.ImplicitSolventNoWorks 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ImplicitSolventNoWorks (27 ms) 29: [ RUN ] GetIrTest.ImplicitSolventYesWorks 29: [ OK ] GetIrTest.ImplicitSolventYesWorks (11 ms) 29: [ RUN ] GetIrTest.HandlesMimic 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp, line 3]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.HandlesMimic (39 ms) 29: [----------] 12 tests from GetIrTest (398 ms total) 29: 29: [----------] 5 tests from SolvateTest 29: [ RUN ] SolvateTest.cs_box_Works 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 1x1x1 boxes 29: Solvent box contains 270 atoms in 90 residues 29: Removed 129 solvent atoms due to solvent-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 47 residues 29: Generated solvent containing 141 atoms in 47 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 29: 29: Output configuration contains 141 atoms in 47 residues 29: Volume : 1.331 (nm^3) 29: Density : 1056.36 (g/l) 29: Number of solvent molecules: 47 29: 29: [ OK ] SolvateTest.cs_box_Works (175 ms) 29: [ RUN ] SolvateTest.cs_cp_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 886 residues 29: Generated solvent containing 2658 atoms in 886 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 29: 29: Output configuration contains 2664 atoms in 888 residues 29: Volume : 27.2709 (nm^3) 29: Density : 974.777 (g/l) 29: Number of solvent molecules: 886 29: 29: [ OK ] SolvateTest.cs_cp_Works (104 ms) 29: [ RUN ] SolvateTest.cs_cp_p_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 886 residues 29: Generated solvent containing 2658 atoms in 886 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 29: 29: Output configuration contains 2664 atoms in 888 residues 29: Volume : 27.2709 (nm^3) 29: Density : 974.777 (g/l) 29: Number of solvent molecules: 886 29: 29: Processing topology 29: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works.top) 29: [ OK ] SolvateTest.cs_cp_p_Works (132 ms) 29: [ RUN ] SolvateTest.shell_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 1902 solvent atoms more than 1.000000 nm from solute. 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 252 residues 29: Generated solvent containing 756 atoms in 252 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 29: 29: Output configuration contains 762 atoms in 254 residues 29: Volume : 27.2709 (nm^3) 29: Density : 279.3 (g/l) 29: Number of solvent molecules: 252 29: 29: [ OK ] SolvateTest.shell_Works (83 ms) 29: [ RUN ] SolvateTest.update_Topology_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 3x3x3 boxes 29: Solvent box contains 14952 atoms in 4984 residues 29: Removed 2787 solvent atoms due to solvent-solvent overlap 29: Removed 30 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 2 different molecule types: 29: HOH ( 3 atoms): 1876 residues 29: SOL ( 3 atoms): 2169 residues 29: Generated solvent containing 0 atoms in 0 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 29: 29: Output configuration contains 12141 atoms in 4047 residues 29: Volume : 125 (nm^3) 29: Density : 968.963 (g/l) 29: Number of solvent molecules: 4045 29: 29: Processing topology 29: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 29: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 29: [ OK ] SolvateTest.update_Topology_Works (680 ms) 29: [----------] 5 tests from SolvateTest (1175 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 26 tests from 4 test cases ran. (2246 ms total) 29: [ PASSED ] 26 tests. 29/40 Test #29: GmxPreprocessTests ............... Passed 2.45 sec test 30 Start 30: Pdb2gmxTest 30: Test command: /build/gromacs-2019.1/build/basic/bin/pdb2gmx-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/Pdb2gmxTest.xml" 30: Test timeout computed to be: 480 30: [==========] Running 80 tests from 6 test cases. 30: [----------] Global test environment set-up. 30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (1440 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (1277 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (1105 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (1206 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (1287 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (1270 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (1101 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (946 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (1015 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (1102 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (997 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (896 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (966 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (1377 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (1080 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (959 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (903 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (1081 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (1098 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (931 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (972 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (1125 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (1030 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (938 ms) 30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (26104 ms total) 30: 30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (675 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (624 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (550 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (545 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Marked 37 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 37 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (569 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Marked 53 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 51 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (646 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Marked 36 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 36 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (507 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Marked 33 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 31 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (471 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (646 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (628 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (511 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (467 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Marked 37 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 37 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (517 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Marked 53 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 51 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (653 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Marked 36 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 36 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (508 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Marked 33 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 31 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (553 ms) 30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (9070 ms total) 30: 30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (724 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (621 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (494 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (488 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Marked 39 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 39 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (527 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Marked 57 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 55 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (622 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Marked 38 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 38 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (567 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Marked 35 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 33 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (490 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (540 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (632 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (536 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (475 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Marked 39 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 39 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (579 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Marked 57 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 55 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (671 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Marked 38 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 38 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (847 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Marked 35 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 33 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (525 ms) 30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (9342 ms total) 30: 30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 255, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 691 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 691 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.132 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (1400 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 291, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 788 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 788 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.366 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (1164 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 262, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 727 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 727 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.124 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (1032 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 233, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 634 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 634 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.888 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (915 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 255, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 691 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 691 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.132 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (1333 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 291, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 788 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 788 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.366 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (1440 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 262, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 727 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 727 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.124 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (1064 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 233, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 634 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 634 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.888 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (990 ms) 30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (9338 ms total) 30: 30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 663 dihedrals, 48 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.115 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (1458 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 778 dihedrals, 49 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (1038 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 696 dihedrals, 39 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.130 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (971 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 618 dihedrals, 38 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.885 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (867 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 663 dihedrals, 48 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.115 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (1284 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 778 dihedrals, 49 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (1135 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 696 dihedrals, 39 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.130 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (1041 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 618 dihedrals, 38 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.885 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (953 ms) 30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (8749 ms total) 30: 30: [----------] 8 tests from ChainSep/Pdb2gmxTest 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 258, now 258 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 651 pairs 30: Before cleaning: 661 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 10 cmap torsion pairs 30: There are 661 dihedrals, 46 impropers, 463 angles 30: 648 pairs, 258 bonds and 0 virtual sites 30: Total mass 1882.146 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on changing chain id only (ignoring TER records). 30: 30: Merged chains into joint molecule definitions at 2 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Identified residue PHE6 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Start terminus PHE-6: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 258 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (1039 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 50, now 50 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 123 pairs 30: Before cleaning: 123 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 123 dihedrals, 9 impropers, 88 angles 30: 123 pairs, 50 bonds and 0 virtual sites 30: Total mass 434.421 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 10 donors and 7 acceptors were found. 30: There are 7 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS8 30: NE223 30: MET12 SD55 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 125, now 125 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 317 pairs 30: Before cleaning: 322 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 5 cmap torsion pairs 30: There are 322 dihedrals, 19 impropers, 227 angles 30: 314 pairs, 125 bonds and 0 virtual sites 30: Total mass 846.083 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 258 atoms and 16 residues 30: Total mass in system 1882.146 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on changing chain id only (ignoring TER records). 30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 4 28 30: 2 'B' 7 58 30: 3 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (28 atoms, 4 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 51 atoms 30: Chain time... 30: Processing chain 2 'B' (58 atoms, 7 residues) 30: Identified residue PHE6 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus PHE-6: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 7 residues with 124 atoms 30: Chain time... 30: Processing chain 3 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 51 atoms 4 residues 30: Including chain 2 in system: 124 atoms 7 residues 30: Including chain 3 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (143 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 258, now 258 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 651 pairs 30: Before cleaning: 661 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 10 cmap torsion pairs 30: There are 661 dihedrals, 46 impropers, 463 angles 30: 648 pairs, 258 bonds and 0 virtual sites 30: Total mass 1882.146 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records only (ignoring chain id). 30: 30: Merged chains into joint molecule definitions at 2 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus ILE-9: COO- 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 258 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (921 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 10 donors and 12 acceptors were found. 30: There are 13 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 30: SG9 30: HIS8 NE251 1.055 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 115, now 115 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 288 pairs 30: Before cleaning: 293 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 6 cmap torsion pairs 30: There are 293 dihedrals, 23 impropers, 203 angles 30: 285 pairs, 115 bonds and 0 virtual sites 30: Total mass 888.952 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 60, now 60 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 152 pairs 30: Before cleaning: 152 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 1 cmap torsion pairs 30: There are 152 dihedrals, 5 impropers, 112 angles 30: 152 pairs, 60 bonds and 0 virtual sites 30: Total mass 391.552 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 258 atoms and 16 residues 30: Total mass in system 1882.146 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records only (ignoring chain id). 30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 8 61 30: 2 'B' 3 25 30: 3 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (61 atoms, 8 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus ILE-9: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 8 residues with 114 atoms 30: Chain time... 30: Processing chain 2 'B' (25 atoms, 3 residues) 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 3 residues with 61 atoms 30: Chain time... 30: Processing chain 3 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 114 atoms 8 residues 30: Including chain 2 in system: 61 atoms 3 residues 30: Including chain 3 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (142 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 260, now 260 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 650 pairs 30: Before cleaning: 660 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 8 cmap torsion pairs 30: There are 660 dihedrals, 45 impropers, 466 angles 30: 647 pairs, 260 bonds and 0 virtual sites 30: Total mass 1900.162 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: 30: Merged chains into joint molecule definitions at 3 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Identified residue PHE6 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Start terminus PHE-6: NH3+ 30: End terminus ILE-9: COO- 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 261 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (943 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 50, now 50 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 123 pairs 30: Before cleaning: 123 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 123 dihedrals, 9 impropers, 88 angles 30: 123 pairs, 50 bonds and 0 virtual sites 30: Total mass 434.421 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 6 donors and 4 acceptors were found. 30: There are 3 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 67, now 67 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 164 pairs 30: Before cleaning: 169 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 169 dihedrals, 13 impropers, 118 angles 30: 161 pairs, 67 bonds and 0 virtual sites 30: Total mass 472.547 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 60, now 60 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 152 pairs 30: Before cleaning: 152 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 1 cmap torsion pairs 30: There are 152 dihedrals, 5 impropers, 112 angles 30: 152 pairs, 60 bonds and 0 virtual sites 30: Total mass 391.552 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 261 atoms and 16 residues 30: Total mass in system 1900.162 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: WARNING: Chain identifier 'B' is used in two non-sequential blocks. 30: They will be treated as separate chains unless you reorder your file. 30: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 4 28 30: 2 'B' 4 33 30: 3 'B' 3 25 30: 4 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (28 atoms, 4 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 51 atoms 30: Chain time... 30: Processing chain 2 'B' (33 atoms, 4 residues) 30: Identified residue PHE6 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Start terminus PHE-6: NH3+ 30: End terminus ILE-9: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 66 atoms 30: Chain time... 30: Processing chain 3 'B' (25 atoms, 3 residues) 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 3 residues with 61 atoms 30: Chain time... 30: Processing chain 4 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 51 atoms 4 residues 30: Including chain 2 in system: 66 atoms 4 residues 30: Including chain 3 in system: 61 atoms 3 residues 30: Including chain 4 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (140 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 256, now 256 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 652 pairs 30: Before cleaning: 662 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 12 cmap torsion pairs 30: There are 662 dihedrals, 47 impropers, 460 angles 30: 649 pairs, 256 bonds and 0 virtual sites 30: Total mass 1864.131 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records and chain id changing. 30: 30: Merged chains into joint molecule definitions at 1 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (930 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 14 donors and 15 acceptors were found. 30: There are 20 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 173, now 173 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 441 pairs 30: Before cleaning: 446 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 9 cmap torsion pairs 30: There are 446 dihedrals, 29 impropers, 312 angles 30: 438 pairs, 173 bonds and 0 virtual sites 30: Total mass 1262.488 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 255 atoms and 16 residues 30: Total mass in system 1864.131 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records and chain id changing. 30: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 11 86 30: 2 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (86 atoms, 11 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 11 residues with 172 atoms 30: Chain time... 30: Processing chain 2 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 172 atoms 11 residues 30: Including chain 2 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (149 ms) 30: [----------] 8 tests from ChainSep/Pdb2gmxTest (4407 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 80 tests from 6 test cases ran. (67010 ms total) 30: [ PASSED ] 80 tests. 30/40 Test #30: Pdb2gmxTest ...................... Passed 67.24 sec test 31 Start 31: CorrelationsTest 31: Test command: /build/gromacs-2019.1/build/basic/bin/correlations-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/CorrelationsTest.xml" 31: Test timeout computed to be: 30 31: [==========] Running 11 tests from 2 test cases. 31: [----------] Global test environment set-up. 31: [----------] 10 tests from AutocorrTest 31: [ RUN ] AutocorrTest.EacNormal 31: [ OK ] AutocorrTest.EacNormal (31 ms) 31: [ RUN ] AutocorrTest.EacNoNormalize 31: [ OK ] AutocorrTest.EacNoNormalize (11 ms) 31: [ RUN ] AutocorrTest.EacCos 31: [ OK ] AutocorrTest.EacCos (26 ms) 31: [ RUN ] AutocorrTest.EacVector 31: [ OK ] AutocorrTest.EacVector (34 ms) 31: [ RUN ] AutocorrTest.EacRcross 31: [ OK ] AutocorrTest.EacRcross (28 ms) 31: [ RUN ] AutocorrTest.EacP0 31: [ OK ] AutocorrTest.EacP0 (36 ms) 31: [ RUN ] AutocorrTest.EacP1 31: [ OK ] AutocorrTest.EacP1 (32 ms) 31: [ RUN ] AutocorrTest.EacP2 31: [ OK ] AutocorrTest.EacP2 (45 ms) 31: [ RUN ] AutocorrTest.EacP3 31: [ OK ] AutocorrTest.EacP3 (12 ms) 31: [ RUN ] AutocorrTest.EacP4 31: [ OK ] AutocorrTest.EacP4 (32 ms) 31: [----------] 10 tests from AutocorrTest (287 ms total) 31: 31: [----------] 1 test from ManyAutocorrelationTest 31: [ RUN ] ManyAutocorrelationTest.Empty 31: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 31: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 11 tests from 2 test cases ran. (325 ms total) 31: [ PASSED ] 11 tests. 31/40 Test #31: CorrelationsTest ................. Passed 0.44 sec test 32 Start 32: AnalysisDataUnitTests 32: Test command: /build/gromacs-2019.1/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 32: Test timeout computed to be: 30 32: [==========] Running 69 tests from 14 test cases. 32: [----------] Global test environment set-up. 32: [----------] 3 tests from AnalysisDataInitializationTest 32: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 32: [ OK ] AnalysisDataInitializationTest.BasicInitialization (22 ms) 32: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 32: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 32: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 32: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 32: [----------] 3 tests from AnalysisDataInitializationTest (22 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (27 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 32: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/0 (34 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 32: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/1 (9 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 32: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/2 (11 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 32: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/3 (11 ms total) 32: 32: [----------] 4 tests from AnalysisArrayDataTest 32: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 32: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisArrayDataTest.StorageWorks 32: [ OK ] AnalysisArrayDataTest.StorageWorks (1 ms) 32: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 32: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 32: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 32: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 32: [----------] 4 tests from AnalysisArrayDataTest (2 ms total) 32: 32: [----------] 6 tests from AverageModuleTest 32: [ RUN ] AverageModuleTest.BasicTest 32: [ OK ] AverageModuleTest.BasicTest (34 ms) 32: [ RUN ] AverageModuleTest.HandlesMultipointData 32: [ OK ] AverageModuleTest.HandlesMultipointData (9 ms) 32: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 32: [ OK ] AverageModuleTest.HandlesMultipleDataSets (38 ms) 32: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 32: [ OK ] AverageModuleTest.HandlesDataSetAveraging (24 ms) 32: [ RUN ] AverageModuleTest.CanCustomizeXAxis 32: [ OK ] AverageModuleTest.CanCustomizeXAxis (33 ms) 32: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 32: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (22 ms) 32: [----------] 6 tests from AverageModuleTest (160 ms total) 32: 32: [----------] 2 tests from FrameAverageModuleTest 32: [ RUN ] FrameAverageModuleTest.BasicTest 32: [ OK ] FrameAverageModuleTest.BasicTest (9 ms) 32: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 32: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (9 ms) 32: [----------] 2 tests from FrameAverageModuleTest (18 ms total) 32: 32: [----------] 7 tests from AnalysisHistogramSettingsTest 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 32: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 32: 32: [----------] 2 tests from SimpleHistogramModuleTest 32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (9 ms) 32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (8 ms) 32: [----------] 2 tests from SimpleHistogramModuleTest (17 ms total) 32: 32: [----------] 3 tests from WeightedHistogramModuleTest 32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (19 ms) 32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (14 ms) 32: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 32: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (8 ms) 32: [----------] 3 tests from WeightedHistogramModuleTest (43 ms total) 32: 32: [----------] 3 tests from BinAverageModuleTest 32: [ RUN ] BinAverageModuleTest.ComputesCorrectly 32: [ OK ] BinAverageModuleTest.ComputesCorrectly (18 ms) 32: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 32: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (14 ms) 32: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 32: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (9 ms) 32: [----------] 3 tests from BinAverageModuleTest (41 ms total) 32: 32: [----------] 4 tests from AbstractAverageHistogramTest 32: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 32: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (3 ms) 32: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 32: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (17 ms) 32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (13 ms) 32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (35 ms) 32: [----------] 4 tests from AbstractAverageHistogramTest (69 ms total) 32: 32: [----------] 3 tests from LifetimeModuleTest 32: [ RUN ] LifetimeModuleTest.BasicTest 32: [ OK ] LifetimeModuleTest.BasicTest (14 ms) 32: [ RUN ] LifetimeModuleTest.CumulativeTest 32: [ OK ] LifetimeModuleTest.CumulativeTest (9 ms) 32: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 32: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (22 ms) 32: [----------] 3 tests from LifetimeModuleTest (45 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 69 tests from 14 test cases ran. (483 ms total) 32: [ PASSED ] 69 tests. 32/40 Test #32: AnalysisDataUnitTests ............ Passed 0.64 sec test 33 Start 33: SelectionUnitTests 33: Test command: /build/gromacs-2019.1/build/basic/bin/selection-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/SelectionUnitTests.xml" 33: Test timeout computed to be: 30 33: [==========] Running 190 tests from 10 test cases. 33: [----------] Global test environment set-up. 33: [----------] 1 test from IndexGroupTest 33: [ RUN ] IndexGroupTest.RemovesDuplicates 33: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 33: [----------] 1 test from IndexGroupTest (0 ms total) 33: 33: [----------] 15 tests from IndexBlockTest 33: [ RUN ] IndexBlockTest.CreatesUnknownBlock 33: [ OK ] IndexBlockTest.CreatesUnknownBlock (55 ms) 33: [ RUN ] IndexBlockTest.CreatesAtomBlock 33: [ OK ] IndexBlockTest.CreatesAtomBlock (39 ms) 33: [ RUN ] IndexBlockTest.CreatesResidueBlock 33: [ OK ] IndexBlockTest.CreatesResidueBlock (24 ms) 33: [ RUN ] IndexBlockTest.CreatesMoleculeBlock 33: [ OK ] IndexBlockTest.CreatesMoleculeBlock (30 ms) 33: [ RUN ] IndexBlockTest.CreatesResidueBlockWithCompletion 33: [ OK ] IndexBlockTest.CreatesResidueBlockWithCompletion (32 ms) 33: [ RUN ] IndexBlockTest.CreatesMoleculeBlockWithCompletion 33: [ OK ] IndexBlockTest.CreatesMoleculeBlockWithCompletion (36 ms) 33: [ RUN ] IndexBlockTest.CreatesSingleBlock 33: [ OK ] IndexBlockTest.CreatesSingleBlock (24 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 33: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 33: [----------] 15 tests from IndexBlockTest (241 ms total) 33: 33: [----------] 11 tests from IndexMapTest 33: [ RUN ] IndexMapTest.InitializesAtomBlock 33: [ OK ] IndexMapTest.InitializesAtomBlock (36 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 33: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (50 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 33: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (23 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 33: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (37 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 33: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (9 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 33: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (35 ms) 33: [ RUN ] IndexMapTest.InitializesMoleculeBlock 33: [ OK ] IndexMapTest.InitializesMoleculeBlock (16 ms) 33: [ RUN ] IndexMapTest.MapsSingleBlock 33: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 33: [ RUN ] IndexMapTest.MapsResidueBlocks 33: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms) 33: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 33: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (21 ms) 33: [ RUN ] IndexMapTest.HandlesMultipleRequests 33: [ OK ] IndexMapTest.HandlesMultipleRequests (51 ms) 33: [----------] 11 tests from IndexMapTest (279 ms total) 33: 33: [----------] 15 tests from NeighborhoodSearchTest 33: [ RUN ] NeighborhoodSearchTest.SimpleSearch 33: [ OK ] NeighborhoodSearchTest.SimpleSearch (41 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 33: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (43 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchBox 33: [ OK ] NeighborhoodSearchTest.GridSearchBox (7 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 33: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (24 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 33: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (14 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 33: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (6 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 33: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (8 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 33: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 33: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (118 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 33: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 33: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 33: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 33: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 33: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (9 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 33: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (3 ms) 33: [----------] 15 tests from NeighborhoodSearchTest (273 ms total) 33: 33: [----------] 12 tests from PositionCalculationTest 33: [ RUN ] PositionCalculationTest.ComputesAtomPositions 33: [ OK ] PositionCalculationTest.ComputesAtomPositions (117 ms) 33: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 33: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (2 ms) 33: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 33: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (56 ms) 33: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 33: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (20 ms) 33: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 33: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (32 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (15 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (52 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionMask 33: [ OK ] PositionCalculationTest.ComputesPositionMask (50 ms) 33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (53 ms) 33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (12 ms) 33: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 33: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (15 ms) 33: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 33: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (38 ms) 33: [----------] 12 tests from PositionCalculationTest (464 ms total) 33: 33: [----------] 30 tests from SelectionCollectionTest 33: [ RUN ] SelectionCollectionTest.HandlesNoSelections 33: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 33: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (35 ms) 33: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 33: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 33: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 33: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 33: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (17 ms) 33: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 33: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 33: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions 33: [ OK ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (34 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 33: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 33: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 33: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (1 ms) 33: [----------] 30 tests from SelectionCollectionTest (109 ms total) 33: 33: [----------] 14 tests from SelectionCollectionInteractiveTest 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (13 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 33: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (8 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (2 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (2 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (19 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (25 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (14 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 33: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (19 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (4 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (44 ms) 33: [----------] 14 tests from SelectionCollectionInteractiveTest (156 ms total) 33: 33: [----------] 66 tests from SelectionCollectionDataTest 33: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 33: [ OK ] SelectionCollectionDataTest.HandlesAllNone (16 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 33: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (12 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResnr 33: [ OK ] SelectionCollectionDataTest.HandlesResnr (13 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 33: [ OK ] SelectionCollectionDataTest.HandlesResIndex (37 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 33: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (13 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 33: [ OK ] SelectionCollectionDataTest.HandlesAtomname (22 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 33: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (23 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 33: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (24 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesChain 33: [ OK ] SelectionCollectionDataTest.HandlesChain (15 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMass 33: [ OK ] SelectionCollectionDataTest.HandlesMass (8 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesCharge 33: [ OK ] SelectionCollectionDataTest.HandlesCharge (19 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 33: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (15 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 33: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (8 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 33: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (8 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBeta 33: [ OK ] SelectionCollectionDataTest.HandlesBeta (10 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResname 33: [ OK ] SelectionCollectionDataTest.HandlesResname (7 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (27 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 33: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (22 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 33: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (18 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (18 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (14 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (9 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (26 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (81 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (29 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (7 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 33: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (9 ms) 33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (21 ms) 33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (17 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 33: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (8 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 33: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (17 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (16 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (8 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (10 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (21 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (11 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (8 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 33: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (34 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (8 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (29 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 33: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (14 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 33: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 33: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (7 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 33: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (9 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 33: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (19 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 33: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (13 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 33: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (8 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (9 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (19 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (14 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (16 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 33: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (28 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 33: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (17 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 33: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (23 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 33: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (9 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (27 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (14 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (18 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 33: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (16 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (20 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (13 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (15 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 33: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (23 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (25 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (11 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (2 ms) 33: [----------] 66 tests from SelectionCollectionDataTest (1120 ms total) 33: 33: [----------] 17 tests from SelectionOptionTest 33: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 33: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 33: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 33: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms) 33: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 33: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (1 ms) 33: [ RUN ] SelectionOptionTest.ChecksEmptySelections 33: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms) 33: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 33: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooManySelections 33: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 33: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 33: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesAdjuster 33: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 33: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 33: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 33: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 33: [----------] 17 tests from SelectionOptionTest (12 ms total) 33: 33: [----------] 9 tests from SelectionFileOptionTest 33: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 33: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 33: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 33: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 33: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 33: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 33: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 33: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms) 33: [----------] 9 tests from SelectionFileOptionTest (7 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 190 tests from 10 test cases ran. (2662 ms total) 33: [ PASSED ] 190 tests. 33/40 Test #33: SelectionUnitTests ............... Passed 2.70 sec test 34 Start 34: TrajectoryAnalysisUnitTests 34: Test command: /build/gromacs-2019.1/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 34: Test timeout computed to be: 30 34: [==========] Running 74 tests from 14 test cases. 34: [----------] Global test environment set-up. 34: [----------] 5 tests from ClustsizeTest 34: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 34: There is one group in the index 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 24 34: cmid: 2, cmax: 4, max_size: 6 34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (319 ms) 34: [ RUN ] ClustsizeTest.NoMolShortCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 34: There is one group in the index 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 24 34: cmid: 1, cmax: 6, max_size: 6 34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (13 ms) 34: [ RUN ] ClustsizeTest.MolDefaultCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 2, cmax: 4, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (96 ms) 34: [ RUN ] ClustsizeTest.MolShortCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 1, cmax: 6, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (12 ms) 34: [ RUN ] ClustsizeTest.MolCSize 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 2, cmax: 4, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolCSize (24 ms) 34: [----------] 5 tests from ClustsizeTest (465 ms total) 34: 34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (38 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 34: Reading frames from gro file 'Test system', 8 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (52 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 34: Reading frames from gro file 'Test system', 8 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (7 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms) 34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (98 ms total) 34: 34: [----------] 11 tests from AngleModuleTest 34: [ RUN ] AngleModuleTest.ComputesSimpleAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesSimpleAngles (51 ms) 34: [ RUN ] AngleModuleTest.ComputesDihedrals 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesDihedrals (23 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorPairAngles (9 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (50 ms) 34: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (8 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (9 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 34: Reading frames from gro file 'Test system for different angles', 33 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (9 ms) 34: [ RUN ] AngleModuleTest.ComputesMultipleAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesMultipleAngles (25 ms) 34: [ RUN ] AngleModuleTest.HandlesDynamicSelections 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesDynamicSelections (48 ms) 34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (26 ms) 34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (26 ms) 34: [----------] 11 tests from AngleModuleTest (285 ms total) 34: 34: [----------] 3 tests from DistanceModuleTest 34: [ RUN ] DistanceModuleTest.ComputesDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2: 34: Number of samples: 5 34: Average distance: 1.43246 nm 34: Standard deviation: 0.96700 nm 34: [ OK ] DistanceModuleTest.ComputesDistances (25 ms) 34: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2: 34: Number of samples: 5 34: Average distance: 1.43246 nm 34: Standard deviation: 0.96700 nm 34: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 34: Number of samples: 4 34: Average distance: 1.81066 nm 34: Standard deviation: 0.79289 nm 34: [ OK ] DistanceModuleTest.ComputesMultipleDistances (27 ms) 34: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2 and res_cog x < 2.8: 34: Number of samples: 3 34: Average distance: 1.72076 nm 34: Standard deviation: 1.24839 nm 34: [ OK ] DistanceModuleTest.HandlesDynamicSelections (20 ms) 34: [----------] 3 tests from DistanceModuleTest (72 ms total) 34: 34: [----------] 2 tests from FreeVolumeModuleTest 34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for 40 particles. These were set to zero. 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: cutoff = 0.18 nm 34: probe_radius = 0 nm 34: seed = 13 34: ninsert = 1000 probes per nm^3 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 34: van der Spoel and Luciano T. Costa 34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Free volume 38.02 +/- 0.00 % 34: Total volume 68.92 +/- 0.00 nm^3 34: Number of molecules 340 total mass 63491.38 Dalton 34: Average molar mass: 186.74 Dalton 34: Density rho: 1529.71 +/- 0.00 nm^3 34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 34: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 34: Fractional free volume 0.194 +/- 0.000 34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (476 ms) 34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: cutoff = 0.18 nm 34: probe_radius = 0 nm 34: seed = 17 34: ninsert = 1000 probes per nm^3 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 34: van der Spoel and Luciano T. Costa 34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Free volume 38.48 +/- 0.00 % 34: Total volume 68.92 +/- 0.00 nm^3 34: Number of molecules 340 total mass 63491.38 Dalton 34: Average molar mass: 186.74 Dalton 34: Density rho: 1529.71 +/- 0.00 nm^3 34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 34: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 34: Fractional free volume 0.200 +/- 0.000 34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (305 ms) 34: [----------] 2 tests from FreeVolumeModuleTest (781 ms total) 34: 34: [----------] 7 tests from PairDistanceModuleTest 34: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesAllDistances (9 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (25 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (47 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (8 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (9 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (8 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (9 ms) 34: [----------] 7 tests from PairDistanceModuleTest (115 ms total) 34: 34: [----------] 5 tests from RdfModuleTest 34: [ RUN ] RdfModuleTest.BasicTest 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.BasicTest (116 ms) 34: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 34: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (70 ms) 34: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (77 ms) 34: [ RUN ] RdfModuleTest.CalculatesSurf 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.CalculatesSurf (68 ms) 34: [ RUN ] RdfModuleTest.CalculatesXY 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.CalculatesXY (75 ms) 34: [----------] 5 tests from RdfModuleTest (407 ms total) 34: 34: [----------] 5 tests from SasaModuleTest 34: [ RUN ] SasaModuleTest.BasicTest 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.BasicTest (104 ms) 34: [ RUN ] SasaModuleTest.HandlesSelectedResidues 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesSelectedResidues (54 ms) 34: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (25 ms) 34: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (73 ms) 34: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (60 ms) 34: [----------] 5 tests from SasaModuleTest (320 ms total) 34: 34: [----------] 8 tests from SelectModuleTest 34: [ RUN ] SelectModuleTest.BasicTest 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.BasicTest (64 ms) 34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (17 ms) 34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (20 ms) 34: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (30 ms) 34: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (14 ms) 34: [ RUN ] SelectModuleTest.NormalizesSizes 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.NormalizesSizes (13 ms) 34: [ RUN ] SelectModuleTest.WritesResidueNumbers 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.WritesResidueNumbers (9 ms) 34: [ RUN ] SelectModuleTest.WritesResidueIndices 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.WritesResidueIndices (11 ms) 34: [----------] 8 tests from SelectModuleTest (179 ms total) 34: 34: [----------] 10 tests from SurfaceAreaTest 34: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 34: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 34: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 34: [ OK ] SurfaceAreaTest.ComputesTwoPoints (3 ms) 34: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 34: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (2 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints12 34: [ OK ] SurfaceAreaTest.SurfacePoints12 (10 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints32 34: [ OK ] SurfaceAreaTest.SurfacePoints32 (15 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints42 34: [ OK ] SurfaceAreaTest.SurfacePoints42 (9 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints122 34: [ OK ] SurfaceAreaTest.SurfacePoints122 (20 ms) 34: [ RUN ] SurfaceAreaTest.Computes100Points 34: [ OK ] SurfaceAreaTest.Computes100Points (14 ms) 34: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 34: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (22 ms) 34: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 34: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (16 ms) 34: [----------] 10 tests from SurfaceAreaTest (114 ms total) 34: 34: [----------] 4 tests from TopologyInformation 34: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 34: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 34: [ RUN ] TopologyInformation.WorksWithGroFile 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TopologyInformation.WorksWithGroFile (9 ms) 34: [ RUN ] TopologyInformation.WorksWithPdbFile 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TopologyInformation.WorksWithPdbFile (47 ms) 34: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 34: 34: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp, line 1]: 34: /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 34: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 34: scheme was introduced, but the group scheme was still the default. The 34: default is now the Verlet scheme, so you will observe different behaviour. 34: 34: 34: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: For a correct single-point energy evaluation with nsteps = 0, use 34: continuation = yes to avoid constraining the input coordinates. 34: 34: Setting the LD random seed to 52621653 34: Generated 330891 of the 330891 non-bonded parameter combinations 34: Generating 1-4 interactions: fudge = 0.5 34: Generated 330891 of the 330891 1-4 parameter combinations 34: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 34: 34: NOTE 3 [file lysozyme.top, line 1465]: 34: System has non-zero total charge: 2.000000 34: Total charge should normally be an integer. See 34: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 34: for discussion on how close it should be to an integer. 34: 34: 34: 34: Removing all charge groups because cutoff-scheme=Verlet 34: Number of degrees of freedom in T-Coupling group rest is 465.00 34: 34: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: NVE simulation with an initial temperature of zero: will use a Verlet 34: buffer of 10%. Check your energy drift! 34: 34: 34: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: You are using a plain Coulomb cut-off, which might produce artifacts. 34: You might want to consider using PME electrostatics. 34: 34: 34: 34: There were 5 notes 34: Reading file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.1 (single precision) 34: Reading file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.1 (single precision) 34: Analysing residue names: 34: There are: 10 Protein residues 34: Analysing Protein... 34: This run will generate roughly 0 Mb of data 34: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (924 ms) 34: [----------] 4 tests from TopologyInformation (980 ms total) 34: 34: [----------] 4 tests from TrajectoryModuleTest 34: [ RUN ] TrajectoryModuleTest.BasicTest 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.BasicTest (28 ms) 34: [ RUN ] TrajectoryModuleTest.PlotsXOnly 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.PlotsXOnly (15 ms) 34: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (18 ms) 34: [ RUN ] TrajectoryModuleTest.HandlesNoForces 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.HandlesNoForces (23 ms) 34: [----------] 4 tests from TrajectoryModuleTest (84 ms total) 34: 34: [----------] 5 tests from UnionFinderTest 34: [ RUN ] UnionFinderTest.WorksEmpty 34: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 34: [ RUN ] UnionFinderTest.BasicMerges 34: [ OK ] UnionFinderTest.BasicMerges (0 ms) 34: [ RUN ] UnionFinderTest.LargerMerges 34: [ OK ] UnionFinderTest.LargerMerges (0 ms) 34: [ RUN ] UnionFinderTest.LongRightMerge 34: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 34: [ RUN ] UnionFinderTest.LongLeftMerge 34: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 34: [----------] 5 tests from UnionFinderTest (0 ms total) 34: 34: [----------] 1 test from MappedUnionFinderTest 34: [ RUN ] MappedUnionFinderTest.BasicMerges 34: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 34: [----------] 1 test from MappedUnionFinderTest (0 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 74 tests from 14 test cases ran. (3900 ms total) 34: [ PASSED ] 74 tests. 34/40 Test #34: TrajectoryAnalysisUnitTests ...... Passed 3.94 sec test 35 Start 35: EnergyAnalysisUnitTests 35: Test command: /build/gromacs-2019.1/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 35: Test timeout computed to be: 30 35: [==========] Running 7 tests from 4 test cases. 35: [----------] Global test environment set-up. 35: [----------] 1 test from DhdlTest 35: [ RUN ] DhdlTest.ExtractDhdl 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 35: Reading file /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 35: Note: file tpx version 110, software tpx version 116 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 35: 35: 35: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 35: [ OK ] DhdlTest.ExtractDhdl (200 ms) 35: [----------] 1 test from DhdlTest (201 ms total) 35: 35: [----------] 1 test from OriresTest 35: [ RUN ] OriresTest.ExtractOrires 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 35: Reading file /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 35: Note: file tpx version 111, software tpx version 116 35: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 35: End your selection with 0 35: Selecting all 7 orientation restraints 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 35: [ OK ] OriresTest.ExtractOrires (148 ms) 35: [----------] 1 test from OriresTest (148 ms total) 35: 35: [----------] 3 tests from EnergyTest 35: [ RUN ] EnergyTest.ExtractEnergy 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 35: [ OK ] EnergyTest.ExtractEnergy (43 ms) 35: [ RUN ] EnergyTest.ExtractEnergyByNumber 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 35: Pres. DC -268.49 3 8.52175 13.2804 (bar) 35: [ OK ] EnergyTest.ExtractEnergyByNumber (27 ms) 35: [ RUN ] EnergyTest.ExtractEnergyMixed 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: [ OK ] EnergyTest.ExtractEnergyMixed (23 ms) 35: [----------] 3 tests from EnergyTest (93 ms total) 35: 35: [----------] 2 tests from ViscosityTest 35: [ RUN ] ViscosityTest.EinsteinViscosity 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Pres-XX 20.2092 65 717.193 185.978 (bar) 35: Pres-XY -47.7351 39 372.522 207.456 (bar) 35: Pres-XZ 11.477 31 379.79 6.80818 (bar) 35: Pres-YX -47.7106 39 372.525 207.5 (bar) 35: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 35: Pres-YZ -41.3534 45 401.216 114.663 (bar) 35: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 35: Pres-ZY -41.3119 45 401.196 114.743 (bar) 35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 35: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: [ OK ] ViscosityTest.EinsteinViscosity (26 ms) 35: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Pres-XX 20.2092 65 717.193 185.978 (bar) 35: Pres-XY -47.7351 39 372.522 207.456 (bar) 35: Pres-XZ 11.477 31 379.79 6.80818 (bar) 35: Pres-YX -47.7106 39 372.525 207.5 (bar) 35: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 35: Pres-YZ -41.3534 45 401.216 114.663 (bar) 35: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 35: Pres-ZY -41.3119 45 401.196 114.743 (bar) 35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 35: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: [ OK ] ViscosityTest.EinsteinViscosityIntegral (39 ms) 35: [----------] 2 tests from ViscosityTest (66 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 7 tests from 4 test cases ran. (509 ms total) 35: [ PASSED ] 7 tests. 35/40 Test #35: EnergyAnalysisUnitTests .......... Passed 0.56 sec test 36 Start 36: ToolUnitTests 36: Test command: /build/gromacs-2019.1/build/basic/bin/tool-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/ToolUnitTests.xml" 36: Test timeout computed to be: 30 36: [==========] Running 4 tests from 1 test case. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from ReportMethodsTest 36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 36: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 36: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 36: [ RUN ] ReportMethodsTest.WritesCorrectInformation 36: 36: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp, line 1]: 36: /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 36: scheme was introduced, but the group scheme was still the default. The 36: default is now the Verlet scheme, so you will observe different behaviour. 36: 36: 36: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: For a correct single-point energy evaluation with nsteps = 0, use 36: continuation = yes to avoid constraining the input coordinates. 36: 36: Setting the LD random seed to -637113824 36: Generated 330891 of the 330891 non-bonded parameter combinations 36: Generating 1-4 interactions: fudge = 0.5 36: Generated 330891 of the 330891 1-4 parameter combinations 36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 36: 36: NOTE 3 [file lysozyme.top, line 1465]: 36: System has non-zero total charge: 2.000000 36: Total charge should normally be an integer. See 36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 36: for discussion on how close it should be to an integer. 36: 36: 36: 36: Removing all charge groups because cutoff-scheme=Verlet 36: Number of degrees of freedom in T-Coupling group rest is 465.00 36: 36: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: NVE simulation with an initial temperature of zero: will use a Verlet 36: buffer of 10%. Check your energy drift! 36: 36: 36: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: You are using a plain Coulomb cut-off, which might produce artifacts. 36: You might want to consider using PME electrostatics. 36: 36: 36: 36: There were 5 notes 36: Reading file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.tpr, VERSION 2019.1 (single precision) 36: Analysing residue names: 36: There are: 10 Protein residues 36: Analysing Protein... 36: This run will generate roughly 0 Mb of data 36: [ OK ] ReportMethodsTest.WritesCorrectInformation (760 ms) 36: [ RUN ] ReportMethodsTest.ToolEndToEndTest 36: 36: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp, line 1]: 36: /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 36: scheme was introduced, but the group scheme was still the default. The 36: default is now the Verlet scheme, so you will observe different behaviour. 36: 36: 36: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: For a correct single-point energy evaluation with nsteps = 0, use 36: continuation = yes to avoid constraining the input coordinates. 36: 36: Setting the LD random seed to -1367190488 36: Generated 330891 of the 330891 non-bonded parameter combinations 36: Generating 1-4 interactions: fudge = 0.5 36: Generated 330891 of the 330891 1-4 parameter combinations 36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 36: 36: NOTE 3 [file lysozyme.top, line 1465]: 36: System has non-zero total charge: 2.000000 36: Total charge should normally be an integer. See 36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 36: for discussion on how close it should be to an integer. 36: 36: 36: 36: Removing all charge groups because cutoff-scheme=Verlet 36: Number of degrees of freedom in T-Coupling group rest is 465.00 36: 36: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: NVE simulation with an initial temperature of zero: will use a Verlet 36: buffer of 10%. Check your energy drift! 36: 36: 36: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: You are using a plain Coulomb cut-off, which might produce artifacts. 36: You might want to consider using PME electrostatics. 36: 36: 36: 36: There were 5 notes 36: Reading file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.tpr, VERSION 2019.1 (single precision) 36: Analysing residue names: 36: There are: 10 Protein residues 36: Analysing Protein... 36: This run will generate roughly 0 Mb of data 36: section: Methods 36: subsection: Simulation system 36: A system of 1 molecules (156 atoms) was simulated. 36: 36: subsection: Simulation settings 36: A total of 0 ns were simulated with a time step of 1 fs. 36: Neighbor searching was performed every 10 steps. 36: The Cut-off algorithm was used for electrostatic interactions. 36: with a cut-off of 1 nm. 36: A single cut-off of 1.1 nm was used for Van der Waals interactions. 36: [ OK ] ReportMethodsTest.ToolEndToEndTest (682 ms) 36: [----------] 4 tests from ReportMethodsTest (1442 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 4 tests from 1 test case ran. (1442 ms total) 36: [ PASSED ] 4 tests. 36/40 Test #36: ToolUnitTests .................... Passed 1.49 sec test 37 Start 37: MdrunTests 37: Test command: /build/gromacs-2019.1/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdrunTests.xml" 37: Test timeout computed to be: 600 37: [==========] Running 29 tests from 11 test cases. 37: [----------] Global test environment set-up. 37: [----------] 1 test from GromppTest 37: [ RUN ] GromppTest.EmptyMdpFileWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 1391657162 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 12.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: NVE simulation: will use the initial temperature of 1046.791 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 37: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: [ OK ] GromppTest.EmptyMdpFileWorks (247 ms) 37: [----------] 1 test from GromppTest (247 ms total) 37: 37: [----------] 1 test from ImdTest 37: [ RUN ] ImdTest.ImdCanRun 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]: 37: The Berendsen thermostat does not generate the correct kinetic energy 37: distribution. You might want to consider using the V-rescale thermostat. 37: 37: Setting the LD random seed to 10913225 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Group 'SecondWaterMolecule' with 3 atoms can be activated for interactive molecular dynamics (IMD). 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 50, rlist from 1.121 to 1.344 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: IMD: Enabled. This simulation will accept incoming IMD connections. 37: IMD: You chose a port number < 1. Will automatically assign a free port. 37: IMD: Pulling from IMD remote is enabled (-imdpull). 37: IMD: Turning on IMD - port for incoming requests is 0. 37: IMD: Setting up incoming socket. 37: IMD: Listening for IMD connection on port 42385. 37: IMD: -imdwait not set, starting simulation. 37: starting mdrun 'spc2' 37: 2 steps, 0.0 ps. 37: turning all bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 37: Calculated rlist for 1x1 atom pair-list as 1.134 nm, buffer size 0.134 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.121 nm, buffer size 0.121 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.701 0.351 199.9 37: (ns/day) (hour/ns) 37: Performance: 2.956 8.119 37: [ OK ] ImdTest.ImdCanRun (725 ms) 37: [----------] 1 test from ImdTest (725 ms total) 37: 37: [----------] 2 tests from PmeTest 37: [ RUN ] PmeTest.ReproducesEnergies 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -251232835 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 37: NVE simulation: will use the initial temperature of 1046.791 K for 37: determining the Verlet buffer size 37: 37: Estimate for the relative computational load of the PME mesh part: 1.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 37: The optimal PME mesh load for parallel simulations is below 0.5 37: and for highly parallel simulations between 0.25 and 0.33, 37: for higher performance, increase the cut-off and the PME grid spacing. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: Calculating fourier grid dimensions for X Y Z 37: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.346 0.173 199.8 37: (ns/day) (hour/ns) 37: Performance: 10.490 2.288 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.420 0.210 199.9 37: (ns/day) (hour/ns) 37: Performance: 8.637 2.779 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.406 0.203 199.9 37: (ns/day) (hour/ns) 37: Performance: 8.924 2.689 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10863 ms) 37: [ RUN ] PmeTest.ScalesTheBox 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -522079485 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Searching the wall atom type(s) 37: Number of degrees of freedom in T-Coupling group rest is 13.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: NVE simulation: will use the initial temperature of 966.268 K for 37: determining the Verlet buffer size 37: 37: Estimate for the relative computational load of the PME mesh part: 1.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: The optimal PME mesh load for parallel simulations is below 0.5 37: and for highly parallel simulations between 0.25 and 0.33, 37: for higher performance, increase the cut-off and the PME grid spacing. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 0 steps, 0.0 ps. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.018 0.009 195.9 37: (ns/day) (hour/ns) 37: Performance: 9.567 2.509 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: Calculating fourier grid dimensions for X Y Z 37: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 37: This run will generate roughly 0 Mb of data 37: [ OK ] PmeTest.ScalesTheBox (31472 ms) 37: [----------] 2 tests from PmeTest (42335 ms total) 37: 37: [----------] 1 test from CompelTest 37: [ RUN ] CompelTest.SwapCanRun 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 37: The Berendsen thermostat does not generate the correct kinetic energy 37: distribution. You might want to consider using the V-rescale thermostat. 37: 37: Setting the LD random seed to -261542871 37: Generated 330891 of the 330891 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 330891 of the 330891 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein' 37: Excluding 3 bonded neighbours molecule type 'OCT' 37: Excluding 1 bonded neighbours molecule type 'NA' 37: Excluding 1 bonded neighbours molecule type 'CL' 37: Excluding 3 bonded neighbours molecule type 'Protein' 37: Excluding 3 bonded neighbours molecule type 'OCT' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Split0 group 'Ch0' contains 83 atoms. 37: Split1 group 'Ch1' contains 83 atoms. 37: Solvent group 'SOL' contains 11931 atoms. 37: Swap group 'NA+' contains 19 atoms. 37: Swap group 'CL-' contains 19 atoms. 37: Number of degrees of freedom in T-Coupling group System is 27869.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.1 (single precision) 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: SWAP: Determining initial numbers of ions per compartment. 37: SWAP: Setting pointers for checkpoint writing 37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 37: starting mdrun 'Channel_coco in octane membrane' 37: 2 steps, 0.0 ps. 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 37: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 1 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 4.129 2.065 200.0 37: (ns/day) (hour/ns) 37: Performance: 0.628 38.238 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.1 (single precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: SWAP: Setting pointers for checkpoint writing 37: SWAP: Copying channel fluxes from checkpoint file data 37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 37: starting mdrun 'Channel_coco in octane membrane' 37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 2.872 1.436 200.0 37: (ns/day) (hour/ns) 37: Performance: 0.902 26.598 37: [ OK ] CompelTest.SwapCanRun (6190 ms) 37: [----------] 1 test from CompelTest (6190 ms total) 37: 37: [----------] 6 tests from BondedInteractionsTest 37: [ RUN ] BondedInteractionsTest.NormalBondWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -969247150 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 2 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 12 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 188.2 37: (ns/day) (hour/ns) 37: Performance: 128.324 0.187 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalBondWorks (145 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 444136376 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 2 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 19 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 188.8 37: (ns/day) (hour/ns) 37: Performance: 124.618 0.193 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedBondWorks (130 ms) 37: [ RUN ] BondedInteractionsTest.NormalAngleWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -414126963 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 1 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 21 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 190.0 37: (ns/day) (hour/ns) 37: Performance: 127.467 0.188 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalAngleWorks (14 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1091084908 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 1 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 19 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 188.9 37: (ns/day) (hour/ns) 37: Performance: 117.888 0.204 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (53 ms) 37: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 1937341423 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 22 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 188.8 37: (ns/day) (hour/ns) 37: Performance: 130.402 0.184 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalDihedralWorks (14 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -490159115 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 21 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 189.4 37: (ns/day) (hour/ns) 37: Performance: 110.754 0.217 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (154 ms) 37: [----------] 6 tests from BondedInteractionsTest (510 ms total) 37: 37: [----------] 2 tests from MdrunTerminationTest 37: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1953179510 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 1, rlist from 1.024 to 1 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 100 steps, 0.1 ps. 37: 37: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Core t (s) Wall t (s) (%) 37: Time: 1.591 0.796 200.0 37: (ns/day) (hour/ns) 37: Performance: 0.326 73.667 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.1 (single precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 37: 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.663 0.331 199.9 37: (ns/day) (hour/ns) 37: Performance: 0.782 30.687 37: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (1161 ms) 37: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -103175113 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 1, rlist from 1.024 to 1 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 100 steps, 0.1 ps. 37: 37: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Core t (s) Wall t (s) (%) 37: Time: 1.109 0.555 200.0 37: (ns/day) (hour/ns) 37: Performance: 0.312 77.024 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.1 (single precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 37: 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 37: Checkpoint file is from part 1, new output files will be suffixed '.part0002'. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 1.163 0.582 200.0 37: (ns/day) (hour/ns) 37: Performance: 0.446 53.859 37: [ OK ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend (1155 ms) 37: [----------] 2 tests from MdrunTerminationTest (2316 ms total) 37: 37: [----------] 4 tests from MimicTest 37: [ RUN ] MimicTest.OneQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -338270789 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 58 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.056 0.028 199.6 37: (ns/day) (hour/ns) 37: Performance: 3.062 7.837 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.OneQuantumMol (223 ms) 37: [ RUN ] MimicTest.AllQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -649126500 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 36 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.002 0.001 191.3 37: (ns/day) (hour/ns) 37: Performance: 108.662 0.221 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.AllQuantumMol (108 ms) 37: [ RUN ] MimicTest.TwoQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 634659557 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 36 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.002 0.001 190.9 37: (ns/day) (hour/ns) 37: Performance: 92.659 0.259 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.TwoQuantumMol (51 ms) 37: [ RUN ] MimicTest.BondCuts 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1093716513 37: Generated 2211 of the 2211 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 2211 of the 2211 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 66.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: NVE simulation: will use the initial temperature of 300.368 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/ala.gro' 37: 37: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 24 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.002 0.001 193.6 37: (ns/day) (hour/ns) 37: Performance: 69.610 0.345 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 37: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.BondCuts (241 ms) 37: [----------] 4 tests from MimicTest (623 ms total) 37: 37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 37: Setting the LD random seed to 188177322 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.569 0.285 199.9 37: (ns/day) (hour/ns) 37: Performance: 0.607 39.520 37: Reading frame 0 time 0.000 37: # Atoms 6 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (299 ms) 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 37: Setting the LD random seed to -342243529 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.458 0.229 199.9 37: (ns/day) (hour/ns) 37: Performance: 0.754 31.848 37: Reading frame 0 time 0.000 37: # Atoms 6 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (243 ms) 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 37: Setting the LD random seed to 2142176229 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.592 0.296 199.9 37: (ns/day) (hour/ns) 37: Performance: 0.584 41.128 37: Reading frame 0 time 0.000 37: # Atoms 3 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (311 ms) 37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (853 ms total) 37: 37: [----------] 3 tests from Checking/InitialConstraintsTest 37: [ RUN ] Checking/InitialConstraintsTest.Works/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1284397771 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 1.317 0.659 200.0 37: (ns/day) (hour/ns) 37: Performance: 0.262 91.475 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (730 ms) 37: [ RUN ] Checking/InitialConstraintsTest.Works/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 1390305328 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.431 0.216 199.9 37: (ns/day) (hour/ns) 37: Performance: 0.801 29.976 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (287 ms) 37: [ RUN ] Checking/InitialConstraintsTest.Works/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: Integrator method md-vv-avek is implemented primarily for validation 37: purposes; for molecular dynamics, you should probably be using md or md-vv 37: 37: Setting the LD random seed to -1135682239 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.422 0.211 199.9 37: (ns/day) (hour/ns) 37: Performance: 0.818 29.327 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (289 ms) 37: [----------] 3 tests from Checking/InitialConstraintsTest (1306 ms total) 37: 37: [----------] 3 tests from MdrunCanWrite/Trajectories 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 86014718 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.423 0.211 199.9 37: (ns/day) (hour/ns) 37: Performance: 2.861 8.390 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (289 ms) 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -426053036 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.393 0.197 199.9 37: (ns/day) (hour/ns) 37: Performance: 3.073 7.809 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (276 ms) 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 2130064901 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.380 0.190 199.9 37: (ns/day) (hour/ns) 37: Performance: 3.177 7.554 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (265 ms) 37: [----------] 3 tests from MdrunCanWrite/Trajectories (830 ms total) 37: 37: [----------] 3 tests from MdrunCanWrite/NptTrajectories 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -627144847 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.273 0.136 199.8 37: (ns/day) (hour/ns) 37: Performance: 1.900 12.634 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (210 ms) 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -2070503291 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.413 0.207 199.9 37: (ns/day) (hour/ns) 37: Performance: 1.255 19.124 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (285 ms) 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 1898822486 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.254 0.127 199.8 37: (ns/day) (hour/ns) 37: Performance: 2.042 11.755 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (201 ms) 37: [----------] 3 tests from MdrunCanWrite/NptTrajectories (696 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 29 tests from 11 test cases ran. (56633 ms total) 37: [ PASSED ] 29 tests. 37/40 Test #37: MdrunTests ....................... Passed 56.69 sec test 38 Start 38: MdrunNonIntegratorTests 38: Test command: /build/gromacs-2019.1/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 38: Test timeout computed to be: 600 38: [==========] Running 57 tests from 4 test cases. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -4.7990990e+01 38: Maximum force = 1.8629828e+02 on atom 13 38: Norm of force = 8.7721844e+01 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1876 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 3.02331e+02 on atom 3 38: F-Norm = 1.18024e+02 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -5.5862099e+01 38: Maximum force = 4.2728845e+02 on atom 13 38: Norm of force = 1.8453478e+02 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (622 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 22.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 3.1937714e+02 38: Maximum force = 9.9988643e+03 on atom 9 38: Norm of force = 4.6166996e+03 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (467 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: 38: NOTE 3 [file glycine_vacuo.top, line 12]: 38: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 38: 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 22.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 2.41575e+04 on atom 10 38: F-Norm = 1.18451e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.5174377e+02 38: Maximum force = 7.4208838e+03 on atom 9 38: Norm of force = 3.5693005e+03 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (346 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 3 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -1.5698413e+02 38: Maximum force = 4.5704984e+02 on atom 17 38: Norm of force = 1.8327747e+02 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (112 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 3 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: 38: NOTE 4 [file unknown]: 38: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 1.06801e+03 on atom 28 38: F-Norm = 4.26916e+02 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -1.6941180e+02 38: Maximum force = 2.1832491e+02 on atom 17 38: Norm of force = 7.9220732e+01 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (76 ms) 38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (3499 ms total) 38: 38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents converged to Fmax < 10 in 1 steps 38: Potential Energy = -9.7425699e-01 38: Maximum force = 4.0132303e+00 on atom 1 38: Norm of force = 1.6383944e+00 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (93 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 4.01323e+00 on atom 1 38: F-Norm = 1.63839e+00 38: 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 38: Potential Energy = -9.9064207e-01 38: Maximum force = 2.5781622e+00 on atom 1 38: Norm of force = 1.0525302e+00 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (34 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: WARNING 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: 38: There was 1 warning 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Low-Memory BFGS Minimizer: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: Using 10 BFGS correction steps. 38: 38: F-max = 4.01323e+00 on atom 1 38: F-Norm = 1.63839e+00 38: 38: 38: writing lowest energy coordinates. 38: 38: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 38: Potential Energy = -9.9064207e-01 38: Maximum force = 2.5781622e+00 on atom 1 38: Norm of force = 1.0525302e+00 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (67 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 3.1939697e+02 38: Maximum force = 9.9704248e+03 on atom 9 38: Norm of force = 4.6227540e+03 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (356 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 2.41672e+04 on atom 10 38: F-Norm = 1.19357e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.5625757e+02 38: Maximum force = 7.5018242e+03 on atom 9 38: Norm of force = 3.6139019e+03 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (338 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: WARNING 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: 38: There was 1 warning 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Low-Memory BFGS Minimizer: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: Using 10 BFGS correction steps. 38: 38: F-max = 2.41672e+04 on atom 10 38: F-Norm = 1.19357e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.8472368e+03 38: Maximum force = 2.1261602e+04 on atom 9 38: Norm of force = 1.0198856e+04 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (361 ms) 38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1249 ms total) 38: 38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: NVE simulation: will use the initial temperature of 68.810 K for 38: determining the Verlet buffer size 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.363 0.182 199.9 38: (ns/day) (hour/ns) 38: Performance: 8.085 2.968 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.trr' 38: 38: trr version: GMX_trn_file (single precision) 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.001 193.9 38: (ns/day) (hour/ns) 38: Performance: 1123.786 0.021 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (228 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: NVE simulation: will use the initial temperature of 68.810 K for 38: determining the Verlet buffer size 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.557 0.278 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.276 4.549 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 35 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 194.4 38: (ns/day) (hour/ns) 38: Performance: 870.878 0.028 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (328 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 38: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.511 0.256 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.743 4.179 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 29 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.001 194.3 38: (ns/day) (hour/ns) 38: Performance: 1038.536 0.023 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (300 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.353 0.177 199.9 38: (ns/day) (hour/ns) 38: Performance: 8.321 2.884 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 27 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 194.3 38: (ns/day) (hour/ns) 38: Performance: 801.222 0.030 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (221 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: NVE simulation: will use the initial temperature of 398.997 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 1.315 0.657 199.9 38: (ns/day) (hour/ns) 38: Performance: 2.234 10.743 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.001 194.3 38: (ns/day) (hour/ns) 38: Performance: 1057.431 0.023 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (1935 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: NVE simulation: will use the initial temperature of 398.997 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.708 0.354 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.150 5.783 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 22 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.001 193.9 38: (ns/day) (hour/ns) 38: Performance: 997.505 0.024 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (1038 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 2.550 1.275 200.0 38: (ns/day) (hour/ns) 38: Performance: 1.152 20.835 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 68 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.024 0.012 199.1 38: (ns/day) (hour/ns) 38: Performance: 121.635 0.197 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (2034 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 2.089 1.044 200.0 38: (ns/day) (hour/ns) 38: Performance: 1.406 17.065 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 22 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 194.1 38: (ns/day) (hour/ns) 38: Performance: 935.265 0.026 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (2561 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: NVE simulation: will use the initial temperature of 456.887 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 7 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 7 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.300 0.150 199.8 38: (ns/day) (hour/ns) 38: Performance: 9.790 2.451 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 23 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.003 196.4 38: (ns/day) (hour/ns) 38: Performance: 551.777 0.043 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (225 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: NVE simulation: will use the initial temperature of 456.887 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 7 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 7 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.292 0.146 199.8 38: (ns/day) (hour/ns) 38: Performance: 10.040 2.390 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 30 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.4 38: (ns/day) (hour/ns) 38: Performance: 466.818 0.051 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (227 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 6 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.409 0.205 199.8 38: (ns/day) (hour/ns) 38: Performance: 7.169 3.348 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 32 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.4 38: (ns/day) (hour/ns) 38: Performance: 449.416 0.053 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (343 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 6 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.371 0.185 199.8 38: (ns/day) (hour/ns) 38: Performance: 7.922 3.030 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.3 38: (ns/day) (hour/ns) 38: Performance: 522.483 0.046 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (298 ms) 38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (9738 ms total) 38: 38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.400 0.200 199.8 38: (ns/day) (hour/ns) 38: Performance: 7.338 3.271 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 24 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 186.8 38: (ns/day) (hour/ns) 38: Performance: 345.305 0.070 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (505 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.446 0.223 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.578 3.648 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 188.0 38: (ns/day) (hour/ns) 38: Performance: 392.895 0.061 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (306 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.404 0.202 199.8 38: (ns/day) (hour/ns) 38: Performance: 7.263 3.304 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 24 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 187.4 38: (ns/day) (hour/ns) 38: Performance: 367.314 0.065 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (280 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.574 0.287 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.116 4.691 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 23 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 187.0 38: (ns/day) (hour/ns) 38: Performance: 361.898 0.066 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (382 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.619 0.310 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.741 5.062 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 191.9 38: (ns/day) (hour/ns) 38: Performance: 293.264 0.082 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (405 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.508 0.254 199.8 38: (ns/day) (hour/ns) 38: Performance: 5.780 4.152 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 48 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.063 0.032 198.7 38: (ns/day) (hour/ns) 38: Performance: 46.430 0.517 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (369 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.332 0.166 199.7 38: (ns/day) (hour/ns) 38: Performance: 8.842 2.714 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 188.6 38: (ns/day) (hour/ns) 38: Performance: 371.747 0.065 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (264 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.440 0.220 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.669 3.599 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 184.8 38: (ns/day) (hour/ns) 38: Performance: 409.505 0.059 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (317 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.488 0.244 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.014 3.991 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 25 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 187.5 38: (ns/day) (hour/ns) 38: Performance: 346.081 0.069 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (345 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.417 0.209 199.8 38: (ns/day) (hour/ns) 38: Performance: 7.031 3.414 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 22 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 187.4 38: (ns/day) (hour/ns) 38: Performance: 368.611 0.065 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (295 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.656 0.328 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.477 5.361 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 187.1 38: (ns/day) (hour/ns) 38: Performance: 436.581 0.055 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (409 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.959 0.480 199.9 38: (ns/day) (hour/ns) 38: Performance: 3.062 7.839 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 15 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 187.9 38: (ns/day) (hour/ns) 38: Performance: 437.884 0.055 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (556 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.799 0.400 199.9 38: (ns/day) (hour/ns) 38: Performance: 3.673 6.533 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 54 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.015 0.008 193.1 38: (ns/day) (hour/ns) 38: Performance: 192.729 0.125 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (505 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.580 0.290 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.062 4.741 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 24 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 187.1 38: (ns/day) (hour/ns) 38: Performance: 342.693 0.070 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (394 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 1.050 0.525 199.9 38: (ns/day) (hour/ns) 38: Performance: 2.797 8.580 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 39 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.207 0.104 199.4 38: (ns/day) (hour/ns) 38: Performance: 14.175 1.693 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (739 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.921 0.461 199.9 38: (ns/day) (hour/ns) 38: Performance: 3.187 7.530 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 187.5 38: (ns/day) (hour/ns) 38: Performance: 409.342 0.059 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (575 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.478 0.239 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.140 3.909 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 186.7 38: (ns/day) (hour/ns) 38: Performance: 399.002 0.060 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (328 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.497 0.249 199.8 38: (ns/day) (hour/ns) 38: Performance: 5.905 4.064 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 23 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 186.9 38: (ns/day) (hour/ns) 38: Performance: 366.811 0.065 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (340 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.587 0.294 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.997 4.803 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 24 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 186.9 38: (ns/day) (hour/ns) 38: Performance: 352.275 0.068 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (377 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.476 0.238 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.171 3.889 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 16 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 185.9 38: (ns/day) (hour/ns) 38: Performance: 410.761 0.058 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (333 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.439 0.220 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.679 3.593 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 187.3 38: (ns/day) (hour/ns) 38: Performance: 362.452 0.066 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (300 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.493 0.247 199.8 38: (ns/day) (hour/ns) 38: Performance: 5.956 4.029 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 25 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 187.4 38: (ns/day) (hour/ns) 38: Performance: 340.986 0.070 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (329 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.654 0.327 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.486 5.350 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 187.5 38: (ns/day) (hour/ns) 38: Performance: 399.468 0.060 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (455 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.597 0.299 199.8 38: (ns/day) (hour/ns) 38: Performance: 4.915 4.883 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 45 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 193.3 38: (ns/day) (hour/ns) 38: Performance: 271.955 0.088 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (598 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 1.646 0.823 200.0 38: (ns/day) (hour/ns) 38: Performance: 1.784 13.454 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 184.5 38: (ns/day) (hour/ns) 38: Performance: 392.745 0.061 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (955 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.523 0.262 199.8 38: (ns/day) (hour/ns) 38: Performance: 5.609 4.279 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 23 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 187.3 38: (ns/day) (hour/ns) 38: Performance: 353.002 0.068 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (383 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.578 0.289 199.8 38: (ns/day) (hour/ns) 38: Performance: 5.075 4.729 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 24 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 190.0 38: (ns/day) (hour/ns) 38: Performance: 357.343 0.067 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (429 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.588 0.294 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.988 4.811 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 19 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 187.1 38: (ns/day) (hour/ns) 38: Performance: 368.214 0.065 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (421 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.480 0.240 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.113 3.926 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 187.4 38: (ns/day) (hour/ns) 38: Performance: 398.383 0.060 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (366 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 1.221 0.611 199.9 38: (ns/day) (hour/ns) 38: Performance: 2.405 9.977 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 187.7 38: (ns/day) (hour/ns) 38: Performance: 392.469 0.061 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (755 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.589 0.295 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.980 4.819 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 191.2 38: (ns/day) (hour/ns) 38: Performance: 313.325 0.077 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (423 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.586 0.293 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.008 4.793 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 186.6 38: (ns/day) (hour/ns) 38: Performance: 397.176 0.060 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (414 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.652 0.326 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.505 5.328 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 24 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 188.5 38: (ns/day) (hour/ns) 38: Performance: 351.331 0.068 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (446 ms) 38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (14302 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 57 tests from 4 test cases ran. (28788 ms total) 38: [ PASSED ] 57 tests. 38/40 Test #38: MdrunNonIntegratorTests .......... Passed 29.07 sec test 39 Start 39: LegacyGroupSchemeMdrunTests 39: Test command: /build/gromacs-2019.1/build/basic/bin/legacy-mdrun-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/LegacyGroupSchemeMdrunTests.xml" 39: Test timeout computed to be: 600 39: [==========] Running 2 tests from 1 test case. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from Simple/TpiTest 39: [ RUN ] Simple/TpiTest.ReproducesOutput/0 39: 39: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0_input.mdp]: 39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be 39: removed in a future release when all interaction forms are supported for 39: the verlet scheme. The verlet scheme already scales better, and it is 39: compatible with GPUs and other accelerators. 39: 39: Generated 331705 of the 331705 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 331705 of the 331705 1-4 parameter combinations 39: Excluding 2 bonded neighbours molecule type 'SOL' 39: Excluding 3 bonded neighbours molecule type 'methane' 39: Number of degrees of freedom in T-Coupling group System is 1308.00 39: 39: There was 1 note 39: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2019.1 (single precision) 39: Using 1 MPI thread 39: 39: 39: NOTE: Thread affinity was not set. 39: 39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be 39: removed in a future release when 'verlet' supports all interaction forms. 39: 39: Reading frames from gro file '216 water molecules', 648 atoms. 39: Reading frame 0 time 0.000 mu 8.698e+02 8.698e+02 39: Last frame 0 time 0.000 39: Analysing residue names: 39: There are: 216 Water residues 39: There are: 1 Other residues 39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm 39: Largest charge group radii for Coulomb: 0.100, 0.100 nm 39: This run will generate roughly 0 Mb of data 39: [ OK ] Simple/TpiTest.ReproducesOutput/0 (785 ms) 39: [ RUN ] Simple/TpiTest.ReproducesOutput/1 39: 39: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1_input.mdp]: 39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be 39: removed in a future release when all interaction forms are supported for 39: the verlet scheme. The verlet scheme already scales better, and it is 39: compatible with GPUs and other accelerators. 39: 39: Generated 331705 of the 331705 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 331705 of the 331705 1-4 parameter combinations 39: Excluding 2 bonded neighbours molecule type 'SOL' 39: Excluding 3 bonded neighbours molecule type 'methane' 39: Number of degrees of freedom in T-Coupling group System is 1308.00 39: 39: There was 1 note 39: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2019.1 (single precision) 39: Using 1 MPI thread 39: 39: 39: NOTE: Thread affinity was not set. 39: 39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be 39: removed in a future release when 'verlet' supports all interaction forms. 39: 39: Reading frames from gro file '216 water molecules', 648 atoms. 39: Reading frame 0 time 0.000 mu 9.151e+01 9.151e+01 39: Last frame 0 time 0.000 39: Analysing residue names: 39: There are: 216 Water residues 39: There are: 1 Other residues 39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm 39: Largest charge group radii for Coulomb: 0.100, 0.100 nm 39: This run will generate roughly 0 Mb of data 39: [ OK ] Simple/TpiTest.ReproducesOutput/1 (701 ms) 39: [----------] 2 tests from Simple/TpiTest (1486 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 2 tests from 1 test case ran. (1486 ms total) 39: [ PASSED ] 2 tests. 39/40 Test #39: LegacyGroupSchemeMdrunTests ...... Passed 1.63 sec test 40 Start 40: MdrunMpiTests 40: Test command: /build/gromacs-2019.1/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdrunMpiTests.xml" 40: Test timeout computed to be: 600 40: [==========] Running 21 tests from 7 test cases. 40: [----------] Global test environment set-up. 40: [----------] 1 test from DomainDecompositionSpecialCasesTest 40: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 1343874970 40: Generated 3 of the 3 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 3 of the 3 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 9.00 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting mdrun 'spc2' 40: 0 steps, 0.0 ps. 40: 40: NOTE: 42 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.001 0.001 169.4 40: (ns/day) (hour/ns) 40: Performance: 119.128 0.201 40: This run will generate roughly 0 Mb of data 40: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (73 ms) 40: [----------] 1 test from DomainDecompositionSpecialCasesTest (73 ms total) 40: 40: [----------] 4 tests from MimicTest 40: [ RUN ] MimicTest.OneQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 1043454179 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 38 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.002 0.001 191.6 40: (ns/day) (hour/ns) 40: Performance: 97.468 0.246 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.OneQuantumMol (36 ms) 40: [ RUN ] MimicTest.AllQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 451308292 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 53 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.002 0.001 193.3 40: (ns/day) (hour/ns) 40: Performance: 70.408 0.341 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.AllQuantumMol (26 ms) 40: [ RUN ] MimicTest.TwoQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 711564780 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 36 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.002 0.001 191.3 40: (ns/day) (hour/ns) 40: Performance: 105.468 0.228 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.TwoQuantumMol (27 ms) 40: [ RUN ] MimicTest.BondCuts 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 40261021 40: Generated 2211 of the 2211 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2211 of the 2211 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 66.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: NVE simulation: will use the initial temperature of 300.368 K for 40: determining the Verlet buffer size 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/ala.gro' 40: 40: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 26 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.002 0.001 194.5 40: (ns/day) (hour/ns) 40: Performance: 70.298 0.341 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 40: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.BondCuts (45 ms) 40: [----------] 4 tests from MimicTest (134 ms total) 40: 40: [----------] 1 test from MultiSimTerminationTest 40: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 40: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 40: [----------] 1 test from MultiSimTerminationTest (0 ms total) 40: 40: [----------] 2 tests from PmeTest 40: [ RUN ] PmeTest.ReproducesEnergies 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: Setting the LD random seed to -1865379236 40: Generated 279 of the 1225 non-bonded parameter combinations 40: Excluding 2 bonded neighbours molecule type 'Methanol' 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 12.00 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 40: NVE simulation: will use the initial temperature of 1046.791 K for 40: determining the Verlet buffer size 40: 40: Estimate for the relative computational load of the PME mesh part: 1.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 40: The optimal PME mesh load for parallel simulations is below 0.5 40: and for highly parallel simulations between 0.25 and 0.33, 40: for higher performance, increase the cut-off and the PME grid spacing. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: Calculating fourier grid dimensions for X Y Z 40: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 40: This run will generate roughly 0 Mb of data 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.584 0.292 199.9 40: (ns/day) (hour/ns) 40: Performance: 6.208 3.866 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.705 0.353 199.9 40: (ns/day) (hour/ns) 40: Performance: 5.145 4.665 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.424 0.212 199.9 40: (ns/day) (hour/ns) 40: Performance: 8.557 2.805 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10946 ms) 40: [ RUN ] PmeTest.ScalesTheBox 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 1087666157 40: Generated 279 of the 1225 non-bonded parameter combinations 40: Excluding 2 bonded neighbours molecule type 'Methanol' 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Searching the wall atom type(s) 40: Number of degrees of freedom in T-Coupling group rest is 13.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: NVE simulation: will use the initial temperature of 966.268 K for 40: determining the Verlet buffer size 40: 40: Estimate for the relative computational load of the PME mesh part: 1.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: The optimal PME mesh load for parallel simulations is below 0.5 40: and for highly parallel simulations between 0.25 and 0.33, 40: for higher performance, increase the cut-off and the PME grid spacing. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting mdrun 'spc-and-methanol' 40: 0 steps, 0.0 ps. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.073 0.037 198.8 40: (ns/day) (hour/ns) 40: Performance: 2.360 10.168 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: Calculating fourier grid dimensions for X Y Z 40: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 40: This run will generate roughly 0 Mb of data 40: [ OK ] PmeTest.ScalesTheBox (31281 ms) 40: [----------] 2 tests from PmeTest (42228 ms total) 40: 40: [----------] 1 test from ReplicaExchangeTerminationTest 40: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 40: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 40: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total) 40: 40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 330891 of the 330891 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 330891 of the 330891 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -4.7990990e+01 40: Maximum force = 1.8629828e+02 on atom 13 40: Norm of force = 8.7721844e+01 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2946 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 330891 of the 330891 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 330891 of the 330891 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 3.02331e+02 on atom 3 40: F-Norm = 1.18024e+02 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -5.5862099e+01 40: Maximum force = 4.2728845e+02 on atom 13 40: Norm of force = 1.8453478e+02 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (910 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 22.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 3.1937714e+02 40: Maximum force = 9.9988643e+03 on atom 9 40: Norm of force = 4.6166996e+03 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (310 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: 40: NOTE 3 [file glycine_vacuo.top, line 12]: 40: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 40: 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 22.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 2.41575e+04 on atom 10 40: F-Norm = 1.18451e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.5174377e+02 40: Maximum force = 7.4208838e+03 on atom 9 40: Norm of force = 3.5693005e+03 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (319 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 2145 of the 2145 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2145 of the 2145 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 40: 40: NOTE 3 [file unknown]: 40: You are using constraints on all bonds, whereas the forcefield has been 40: parametrized only with constraints involving hydrogen atoms. We suggest 40: using constraints = h-bonds instead, this will also improve performance. 40: 40: Cleaning up constraints and constant bonded interactions with virtual sites 40: Removed 18 Angles with virtual sites, 21 left 40: Removed 10 Proper Dih.s with virtual sites, 44 left 40: Converted 15 Constraints with virtual sites to connections, 7 left 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 23.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -1.5698413e+02 40: Maximum force = 4.5704984e+02 on atom 17 40: Norm of force = 1.8327747e+02 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (320 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 2145 of the 2145 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2145 of the 2145 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 40: 40: NOTE 3 [file unknown]: 40: You are using constraints on all bonds, whereas the forcefield has been 40: parametrized only with constraints involving hydrogen atoms. We suggest 40: using constraints = h-bonds instead, this will also improve performance. 40: 40: 40: NOTE 4 [file unknown]: 40: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 40: 40: Cleaning up constraints and constant bonded interactions with virtual sites 40: Removed 18 Angles with virtual sites, 21 left 40: Removed 10 Proper Dih.s with virtual sites, 44 left 40: Converted 15 Constraints with virtual sites to connections, 7 left 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 23.00 40: 40: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 5 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 1.06801e+03 on atom 28 40: F-Norm = 4.26916e+02 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -1.6941180e+02 40: Maximum force = 2.1832491e+02 on atom 17 40: Norm of force = 7.9220732e+01 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (422 ms) 40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (5228 ms total) 40: 40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents converged to Fmax < 10 in 1 steps 40: Potential Energy = -9.7425699e-01 40: Maximum force = 4.0132303e+00 on atom 1 40: Norm of force = 1.6383944e+00 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (110 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 4.01323e+00 on atom 1 40: F-Norm = 1.63839e+00 40: 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 40: Potential Energy = -9.9064207e-01 40: Maximum force = 2.5781622e+00 on atom 1 40: Norm of force = 1.0525302e+00 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (179 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: 40: WARNING 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: 40: There was 1 warning 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 40: 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Low-Memory BFGS Minimizer: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: Using 10 BFGS correction steps. 40: 40: F-max = 4.01323e+00 on atom 1 40: F-Norm = 1.63839e+00 40: 40: 40: writing lowest energy coordinates. 40: 40: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 40: Potential Energy = -9.9064207e-01 40: Maximum force = 2.5781622e+00 on atom 1 40: Norm of force = 1.0525302e+00 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (105 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 3.1939697e+02 40: Maximum force = 9.9704248e+03 on atom 9 40: Norm of force = 4.6227540e+03 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (454 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 2.41672e+04 on atom 10 40: F-Norm = 1.19357e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.5625757e+02 40: Maximum force = 7.5018242e+03 on atom 9 40: Norm of force = 3.6139019e+03 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (275 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: 40: WARNING 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: 40: There was 1 warning 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 40: 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Low-Memory BFGS Minimizer: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: Using 10 BFGS correction steps. 40: 40: F-max = 2.41672e+04 on atom 10 40: F-Norm = 1.19357e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.8472368e+03 40: Maximum force = 2.1261602e+04 on atom 9 40: Norm of force = 1.0198856e+04 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (306 ms) 40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1430 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 21 tests from 7 test cases ran. (49093 ms total) 40: [ PASSED ] 21 tests. 40: 40: YOU HAVE 4 DISABLED TESTS 40: 40/40 Test #40: MdrunMpiTests .................... Passed 49.29 sec 100% tests passed, 0 tests failed out of 40 Label Time Summary: GTest = 241.85 sec*proc (40 tests) IntegrationTest = 138.14 sec*proc (5 tests) MpiTest = 0.74 sec*proc (3 tests) SlowTest = 67.24 sec*proc (1 test) UnitTest = 36.47 sec*proc (34 tests) Total Test time (real) = 245.32 sec /usr/bin/make -j3 -C build/basic-dp tests make[1]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles 84 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/external/googletest /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/external/googletest /build/gromacs-2019.1/build/basic-dp/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 0%] Built target mdrun_test_objlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 1%] Built target tng_io_obj /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 4%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 4%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 17%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 19%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp Scanning dependencies of target gmock make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googlemock/src/gmock-all.cc Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 19%] Built target mdrunutility-test-shared [ 19%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend cd /build/gromacs-2019.1/build/basic-dp/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googletest/src/gtest-all.cc make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/datatest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/mock_datamodule.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/analysisdata/tests/datatest.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/tests/datatest.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValueAndError(int, int, real, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::test::AnalysisDataTestInputFrame}; _Tp = gmx::test::AnalysisDataTestInputFrame; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'gmx::test::AnalysisDataTestInputFrame& gmx::test::AnalysisDataTestInput::addFrame(real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValueAndError(real, real, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 19%] Built target analysisdata-test-shared /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make 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/build/gromacs-2019.1/src/external/tinyxml2/tinyxml2.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi-printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata-xml.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 80%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/testutils/tests /build/gromacs-2019.1/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/testutils/tests /build/gromacs-2019.1/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= Scanning dependencies of target testutils-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/mpitest.cpp Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/interactivetest.cpp Scanning dependencies of target mdrun-non-integrator-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 80%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/refdata_tests.cpp Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/mdebin.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/rerun.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/testasserts_tests.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/settle.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/settle.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::SettleTest_SatisfiesConstraints_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/settle.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp:37: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/topology/block.h:42, from /build/gromacs-2019.1/src/gromacs/mdlib/shake.h:48, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-non-integrator-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/include/c++/8/bits/vector.tcc: In function 'void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector&, const std::vector&, const std::vector&, const std::vector&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 82%] Built target testutils-test /usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target applied-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 83%] Built target mdrun-non-integrator-test /usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target listed-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/tests/bonded.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp:46: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/simulationsignal.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp:46: /usr/include/c++/8/bits/stl_vector.h: In function 'void {anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 83%] Built target listed-forces-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/commandline/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp [ 83%] Built target applied-forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/domdec/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/hashedmap.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroups.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroups.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/localatomsetmanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp:173:28: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 updateGroupsCog.addCogs(globalAtomIndices, positions); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp:173:28: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 84%] Built target mdlib-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/ewald/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 84%] Built target domdec-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fft/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmebsplinetest.cpp Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 85%] Built target fft-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock.h:58, from /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 vector(initializer_list __l, ^~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock.h:58, from /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock.h:58, from /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:97:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }; ^ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:165:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }; ^ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:174:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }; ^ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineparser.cpp In file included from /usr/include/c++/8/map:61, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock.h:58, from /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp:47: /usr/include/c++/8/bits/stl_map.h: In function 'std::map<_Key, _Tp, _Compare, _Alloc>::map(std::initializer_list >, const _Compare&, const allocator_type&) [with _Key = gmx::BasicVector; _Tp = t_complex; _Compare = std::less >; _Alloc = std::allocator, t_complex> >]': /usr/include/c++/8/bits/stl_map.h:226:7: note: parameter passing for argument of type 'std::initializer_list, t_complex> >' changed in GCC 7.1 map(initializer_list __l, ^~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp:343:1: note: parameter passing for argument of type 'std::initializer_list, t_complex> >' changed in GCC 7.1 }; ^ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp:343:1: note: parameter passing for argument of type 'std::initializer_list, t_complex> >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:43: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test::TestBody() [with gtest_TypeParam_ = double]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:57: /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void compareViews(ArrayRef input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void runTest(const gmx_gpu_info_t &gpuInfo, ^~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test::TestBody() [with gtest_TypeParam_ = double]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:57: /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef >, gmx::ArrayRef >) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void compareViews(ArrayRef < BasicVector < T>> input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef, gmx::ArrayRef) [with T = gmx::BasicVector]': /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void runTest(const gmx_gpu_info_t &gpuInfo, ^~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:43: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector, gmx::Allocator, gmx::HostAllocationPolicy> >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test::TestBody() [with gtest_TypeParam_ = gmx::BasicVector]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test::TestBody() [with gtest_TypeParam_ = gmx::BasicVector]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/pargs.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock.h:58, from /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; = void; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 vector(_InputIterator __first, _InputIterator __last, ^~~~~~ /usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:326:114: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 CoordinatesVector const c_sampleCoordinates1(c_sampleCoordinatesFull.begin(), c_sampleCoordinatesFull.begin() + 1); ^ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:328:118: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 CoordinatesVector const c_sampleCoordinates2(c_sampleCoordinatesFull.begin() + 1, c_sampleCoordinatesFull.begin() + 3); ^ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:330:120: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 CoordinatesVector const c_sampleCoordinates13(c_sampleCoordinatesFull.begin() + 3, c_sampleCoordinatesFull.begin() + 16); ^ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmetestcommon.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 86%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/hardware/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 88%] Built target commandline-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/testhardwarecontexts.cpp Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/math/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 88%] Built target ewald-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 88%] Built target hardware-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/math/arrayrefwithpadding.h:49, from /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp:43: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/math/arrayrefwithpadding.h:49, from /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp:49: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 88%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp:50: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::RVecTest_ConvertsImplicitlyFrom_rvec_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 88%] Built target mdrunutility-mpi-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/options/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= In file included from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:59: /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef >, int) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void fillInputContents(ArrayRef < BasicVector < T>> inputRef, ^~~~~~~~~~~~~~~~~ Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/abstractoptionstorage.cpp /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void compareViews(ArrayRef input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef >, gmx::ArrayRef >) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void compareViews(ArrayRef < BasicVector < T>> input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpmanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector, gmx::Allocator, gmx::AlignedAllocationPolicy> >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector, std::allocator > >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 88%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/random/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoption.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 89%] Built target math-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/restraint/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/tests/manager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 89%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tables/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoptionmanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}}, ^~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}}, ^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/option.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/seed.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 89%] Built target table-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp In file included from /usr/include/c++/8/vector:64, from /usr/include/c++/8/bits/random.h:34, from /usr/include/c++/8/random:49, from /build/gromacs-2019.1/src/gromacs/random/seed.h:51, from /build/gromacs-2019.1/src/gromacs/random/threefry.h:51, from /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 vector(initializer_list __l, ^~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/repeatingsection.cpp /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformintdistribution.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 89%] Built target taskassignment-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 89%] Built target utility-mpi-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/timeunitmanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/treesupport.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 90%] Built target random-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fileio/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp:48: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 91%] Built target options-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/tngio.cpp /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/pulling/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 91%] Built target fileio-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/awh/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 91%] Built target pull-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/simd/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/base.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_vector_operations.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.h:57, from /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, double, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_vector_operations.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 92%] Built target awh-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/compat/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/make_unique.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 92%] Built target compat-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxana/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxana-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/entropy.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.h:46, from /build/gromacs-2019.1/src/gromacs/gmxana/tests/entropy.cpp:43: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/gmxana/thermochemistry.h:46, from /build/gromacs-2019.1/src/gromacs/gmxana/tests/entropy.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::Entropy_QuasiHarmonic_300_NoLinear_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::Entropy_Schlitter_300_NoLinear_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::Entropy_Schlitter_300_Linear_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::Entropy_QuasiHarmonic_200_NoLinear_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::Entropy_QuasiHarmonic_200_Linear_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_trjconv.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_msd.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 95%] Built target simd-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 96%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxpreprocess-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask64.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 96%] Built target pdb2gmx-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= Scanning dependencies of target correlations-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/commandline/pargs.h:47, from /build/gromacs-2019.1/src/gromacs/correlationfunctions/autocorr.h:53, from /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/autocorr.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP0_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [ 96%] Built target gmxpreprocess-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP4_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNormal_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNoNormalize_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP3_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP1_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP2_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacCos_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacVector_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacRcross_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/correlationdataset.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask128.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 96%] Built target correlations-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/selection/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= Scanning dependencies of target selection-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/indexutil.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/nbsearch.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/gmxregex.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/average.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/selection/nbsearch.h:52, from /build/gromacs-2019.1/src/gromacs/selection/tests/nbsearch.cpp:49: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double (&)[3]}; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'gmx::AnalysisNeighborhoodPositions {anonymous}::NeighborhoodSearchTestData::testPositions() const': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTest::testPairSearch(gmx::AnalysisNeighborhoodSearch*, const {anonymous}::NeighborhoodSearchTestData&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector}; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/logger.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSelfPairsSearch_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesConcurrentSearches_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomRefPositions(int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNoPBC_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNullPBC_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesSkippingPairs_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/poscalc.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/histogram.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/selectioncollection.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/path.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/analysisdata-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 96%] Built target analysisdata-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryanalysis-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/selectionoption.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/toputils.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 97%] Built target utility-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/energyanalysis/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target energyanalysis-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/legacyenergy.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 97%] Built target selection-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tools/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= Scanning dependencies of target tool-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/report-methods.cpp.o -c /build/gromacs-2019.1/src/gromacs/tools/tests/report-methods.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesSinglePoint_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPoints_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPointsOfUnequalRadius_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints12_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints32_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints42_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints122_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_Computes100Points_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_Computes100PointsWithRectangularPBC_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_Computes100PointsWithTriclinicPBC_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp [ 97%] Built target energyanalysis-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/tool-test.dir/report-methods.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 97%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target legacy-mdrun-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/tpitest.cpp Scanning dependencies of target mdrun-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/grompp.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/legacy-mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/legacy-mdrun-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/initialconstraints.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 97%] Built target legacy-mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/interactiveMD.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/pmetest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/trajectoryanalysis-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [100%] Built target trajectoryanalysis-test cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/swapcoords.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/termination.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/multisim.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [100%] Built target mdrun-test cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/pmetest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/replicaexchange.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [100%] Built target mdrun-mpi-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1 /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[1]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/gromacs-2019.1/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 ) UpdateCTestConfiguration from :/build/gromacs-2019.1/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-2019.1/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/basic-dp/DartConfiguration.tcl Test project /build/gromacs-2019.1/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/gromacs-2019.1/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (64 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (70 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariants 1: [ OK ] ReferenceDataTest.HandlesVariants (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (19 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms) 1: [----------] 34 tests from ReferenceDataTest (32 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (23 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (1 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (1 ms) 1: [----------] 4 tests from XvgTests (26 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (128 ms total) 1: [ PASSED ] 59 tests. 1/40 Test #1: TestUtilsUnitTests ............... Passed 1.61 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /build/gromacs-2019.1/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (8 ms) 2: [----------] 1 test from MpiSelfTest (8 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (9 ms total) 2: [ PASSED ] 1 test. 2/40 Test #2: TestUtilsMpiUnitTests ............ Passed 0.14 sec test 3 Start 3: MdlibUnitTest 3: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 3: Test timeout computed to be: 30 3: [==========] Running 50 tests from 8 test cases. 3: [----------] Global test environment set-up. 3: [----------] 1 test from VerletBufferConstraintTest 3: [ RUN ] VerletBufferConstraintTest.EqualMasses 3: [ OK ] VerletBufferConstraintTest.EqualMasses (37 ms) 3: [----------] 1 test from VerletBufferConstraintTest (37 ms total) 3: 3: [----------] 3 tests from PrintEbin 3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (125 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (17 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (9 ms) 3: [----------] 3 tests from PrintEbin (151 ms total) 3: 3: [----------] 4 tests from ShakeTest 3: [ RUN ] ShakeTest.ConstrainsOneBond 3: [ OK ] ShakeTest.ConstrainsOneBond (17 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 3: [----------] 4 tests from ShakeTest (17 ms total) 3: 3: [----------] 1 test from NullSignalTest 3: [ RUN ] NullSignalTest.NullSignallerWorks 3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 3: [----------] 1 test from NullSignalTest (0 ms total) 3: 3: [----------] 7 tests from SignalTest 3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 3: [----------] 7 tests from SignalTest (0 ms total) 3: 3: [----------] 9 tests from UpdateGroups 3: [ RUN ] UpdateGroups.ethaneUA 3: [ OK ] UpdateGroups.ethaneUA (46 ms) 3: [ RUN ] UpdateGroups.methane 3: [ OK ] UpdateGroups.methane (0 ms) 3: [ RUN ] UpdateGroups.ethane 3: [ OK ] UpdateGroups.ethane (11 ms) 3: [ RUN ] UpdateGroups.butaneUA 3: [ OK ] UpdateGroups.butaneUA (0 ms) 3: [ RUN ] UpdateGroups.waterThreeSite 3: [ OK ] UpdateGroups.waterThreeSite (0 ms) 3: [ RUN ] UpdateGroups.waterFourSite 3: [ OK ] UpdateGroups.waterFourSite (0 ms) 3: [ RUN ] UpdateGroups.fourAtomsWithSettle 3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 3: [ RUN ] UpdateGroups.waterFlexAngle 3: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 3: [ RUN ] UpdateGroups.twoMoltypes 3: [ OK ] UpdateGroups.twoMoltypes (0 ms) 3: [----------] 9 tests from UpdateGroups (58 ms total) 3: 3: [----------] 1 test from UpdateGroupsCog 3: [ RUN ] UpdateGroupsCog.ComputesCogs 3: [ OK ] UpdateGroupsCog.ComputesCogs (20 ms) 3: [----------] 1 test from UpdateGroupsCog (20 ms total) 3: 3: [----------] 24 tests from WithParameters/SettleTest 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (31 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (1 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms) 3: [----------] 24 tests from WithParameters/SettleTest (33 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 50 tests from 8 test cases ran. (317 ms total) 3: [ PASSED ] 50 tests. 3/40 Test #3: MdlibUnitTest .................... Passed 0.55 sec test 4 Start 4: AppliedForcesUnitTest 4: Test command: /build/gromacs-2019.1/build/basic-dp/bin/applied-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 4: Test timeout computed to be: 30 4: [==========] Running 3 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 3 tests from ElectricFieldTest 4: [ RUN ] ElectricFieldTest.Static 4: [ OK ] ElectricFieldTest.Static (112 ms) 4: [ RUN ] ElectricFieldTest.Oscillating 4: [ OK ] ElectricFieldTest.Oscillating (0 ms) 4: [ RUN ] ElectricFieldTest.Pulsed 4: [ OK ] ElectricFieldTest.Pulsed (0 ms) 4: [----------] 3 tests from ElectricFieldTest (113 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 3 tests from 1 test case ran. (113 ms total) 4: [ PASSED ] 3 tests. 4/40 Test #4: AppliedForcesUnitTest ............ Passed 0.32 sec test 5 Start 5: ListedForcesTest 5: Test command: /build/gromacs-2019.1/build/basic-dp/bin/listed-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 15 tests from 1 test case. 5: [----------] Global test environment set-up. 5: [----------] 15 tests from BondedTest 5: [ RUN ] BondedTest.BondAnglePbcNone 5: [ OK ] BondedTest.BondAnglePbcNone (46 ms) 5: [ RUN ] BondedTest.BondAnglePbcXy 5: [ OK ] BondedTest.BondAnglePbcXy (25 ms) 5: [ RUN ] BondedTest.BondAnglePbcXyz 5: [ OK ] BondedTest.BondAnglePbcXyz (25 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcNone 5: [ OK ] BondedTest.DihedralAnglePbcNone (25 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXy 5: [ OK ] BondedTest.DihedralAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXyz 5: [ OK ] BondedTest.DihedralAnglePbcXyz (19 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcNo 5: [ OK ] BondedTest.IfuncBondsPbcNo (23 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXy 5: [ OK ] BondedTest.IfuncBondsPbcXy (8 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXyz 5: [ OK ] BondedTest.IfuncBondsPbcXyz (8 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcNo 5: [ OK ] BondedTest.IfuncAnglesPbcNo (8 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXy 5: [ OK ] BondedTest.IfuncAnglesPbcXy (23 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ 5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (19 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo 5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (10 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (39 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (10 ms) 5: [----------] 15 tests from BondedTest (289 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 15 tests from 1 test case ran. (289 ms total) 5: [ PASSED ] 15 tests. 5/40 Test #5: ListedForcesTest ................. Passed 0.48 sec test 6 Start 6: CommandLineUnitTests 6: Test command: /build/gromacs-2019.1/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 6: Test timeout computed to be: 30 6: [==========] Running 55 tests from 6 test cases. 6: [----------] Global test environment set-up. 6: [----------] 3 tests from CommandLineHelpModuleTest 6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (145 ms) 6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (60 ms) 6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (140 ms) 6: [----------] 3 tests from CommandLineHelpModuleTest (345 ms total) 6: 6: [----------] 6 tests from CommandLineHelpWriterTest 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (92 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (36 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (3 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (87 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (16 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (41 ms) 6: [----------] 6 tests from CommandLineHelpWriterTest (276 ms total) 6: 6: [----------] 6 tests from CommandLineModuleManagerTest 6: [ RUN ] CommandLineModuleManagerTest.RunsModule 6: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 6: [----------] 6 tests from CommandLineModuleManagerTest (2 ms total) 6: 6: [----------] 13 tests from CommandLineParserTest 6: [ RUN ] CommandLineParserTest.HandlesSingleValues 6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (47 ms) 6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesString 6: [ OK ] CommandLineParserTest.HandlesString (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (1 ms) 6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (45 ms) 6: [----------] 13 tests from CommandLineParserTest (93 ms total) 6: 6: [----------] 6 tests from CommandLineProgramContextTest 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (39 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (1 ms) 6: [----------] 6 tests from CommandLineProgramContextTest (40 ms total) 6: 6: [----------] 21 tests from ParseCommonArgsTest 6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (1 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (15 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (8 ms) 6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 6: [----------] 21 tests from ParseCommonArgsTest (25 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 55 tests from 6 test cases ran. (781 ms total) 6: [ PASSED ] 55 tests. 6/40 Test #6: CommandLineUnitTests ............. Passed 0.98 sec test 7 Start 7: DomDecTests 7: Test command: /build/gromacs-2019.1/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/DomDecTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 9 tests from 2 test cases. 7: [----------] Global test environment set-up. 7: [----------] 7 tests from HashedMap 7: [ RUN ] HashedMap.InsertsFinds 7: [ OK ] HashedMap.InsertsFinds (0 ms) 7: [ RUN ] HashedMap.NegativeKeysWork 7: [ OK ] HashedMap.NegativeKeysWork (0 ms) 7: [ RUN ] HashedMap.InsertsErases 7: [ OK ] HashedMap.InsertsErases (0 ms) 7: [ RUN ] HashedMap.InsertsOrAssigns 7: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 7: [ RUN ] HashedMap.Clears 7: [ OK ] HashedMap.Clears (0 ms) 7: [ RUN ] HashedMap.LinkedEntries 7: [ OK ] HashedMap.LinkedEntries (0 ms) 7: [ RUN ] HashedMap.ResizesTable 7: [ OK ] HashedMap.ResizesTable (0 ms) 7: [----------] 7 tests from HashedMap (0 ms total) 7: 7: [----------] 2 tests from LocalAtomSetManager 7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 7: [----------] 2 tests from LocalAtomSetManager (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 9 tests from 2 test cases ran. (1 ms total) 7: [ PASSED ] 9 tests. 7/40 Test #7: DomDecTests ...................... Passed 0.34 sec test 8 Start 8: EwaldUnitTests 8: Test command: /build/gromacs-2019.1/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 257 tests from 10 test cases. 8: [----------] Global test environment set-up. 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (178 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (179 ms total) 8: 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (140 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (57 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (27 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (57 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (28 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (59 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (28 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (32 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (20 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (40 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (25 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (21 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (41 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (82 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (24 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (23 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (40 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (9 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (25 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (34 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (25 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (17 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (39 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (33 ms) 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (933 ms total) 8: 8: [----------] 144 tests from SaneInput/PmeGatherTest 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (26 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (19 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (15 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (13 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (33 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (37 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (14 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (18 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (27 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (23 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (33 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (26 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (11 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (18 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (17 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (20 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (15 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (32 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (26 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (10 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (7 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (13 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (35 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (18 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (15 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (21 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (12 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (21 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (24 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (17 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (44 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (36 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (21 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (38 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (34 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (17 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (23 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (34 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (54 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (13 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (24 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (11 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (23 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (38 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (13 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (40 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (60 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (26 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (37 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (5 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (28 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (37 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (49 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (86 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (11 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (18 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (23 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (54 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (28 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (13 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (3 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (74 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (49 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (30 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (41 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (10 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (17 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (28 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (13 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (20 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (32 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (10 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (34 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (31 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (11 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (57 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (41 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (9 ms) 8: [----------] 144 tests from SaneInput/PmeGatherTest (2538 ms total) 8: 8: [----------] 16 tests from SaneInput/PmeSolveTest 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (19 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (45 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (39 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (33 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (51 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (9 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (24 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (4 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (4 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (6 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (20 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (49 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (20 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (25 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (18 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (16 ms) 8: [----------] 16 tests from SaneInput/PmeSolveTest (382 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (8 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (9 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (19 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (24 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (24 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (8 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (8 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (21 ms) 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (121 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (16 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (18 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (14 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (7 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (31 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (34 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (24 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (12 ms) 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (157 ms total) 8: 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (8 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (10 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (18 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (16 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (5 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (10 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (16 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (9 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (18 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (23 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (18 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (11 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (5 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (9 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (8 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (9 ms) 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (194 ms total) 8: 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (21 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (41 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (23 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (8 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (8 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (9 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (35 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (13 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (20 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (32 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (51 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (27 ms) 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (293 ms total) 8: 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (57 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (31 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (34 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (42 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (41 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (19 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (14 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (24 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (9 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (25 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (35 ms) 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (337 ms total) 8: 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (35 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (44 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (113 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (23 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (36 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (43 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (22 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (30 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (63 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (79 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (44 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (43 ms) 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (585 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 257 tests from 10 test cases ran. (6188 ms total) 8: [ PASSED ] 257 tests. 8/40 Test #8: EwaldUnitTests ................... Passed 6.60 sec test 9 Start 9: FFTUnitTests 9: Test command: /build/gromacs-2019.1/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 14 tests from 4 test cases. 9: [----------] Global test environment set-up. 9: [----------] 2 tests from ManyFFTTest 9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (59 ms) 9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (65 ms) 9: [----------] 2 tests from ManyFFTTest (126 ms total) 9: 9: [----------] 1 test from FFTTest 9: [ RUN ] FFTTest.Real2DLength18_15Test 9: [ OK ] FFTTest.Real2DLength18_15Test (20 ms) 9: [----------] 1 test from FFTTest (20 ms total) 9: 9: [----------] 1 test from FFFTest3D 9: [ RUN ] FFFTest3D.Real5_6_9 9: [ OK ] FFFTest3D.Real5_6_9 (49 ms) 9: [----------] 1 test from FFFTest3D (50 ms total) 9: 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (36 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (11 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (10 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (9 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (37 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (28 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (9 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (8 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (18 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (22 ms) 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (189 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 14 tests from 4 test cases ran. (385 ms total) 9: [ PASSED ] 14 tests. 9/40 Test #9: FFTUnitTests ..................... Passed 0.86 sec test 10 Start 10: GpuUtilsUnitTests 10: Test command: /build/gromacs-2019.1/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 60 tests from 19 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Swap 10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Comparison 10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Swap 10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Comparison 10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Swap 10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Comparison 10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Swap 10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Comparison 10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 10: 10: [----------] 1 test from HostAllocatorUntypedTest 10: [ RUN ] HostAllocatorUntypedTest.Comparison 10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.Move 10: [ OK ] AllocatorTest/0.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/0 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.Move 10: [ OK ] AllocatorTest/1.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/1 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/2.Move 10: [ OK ] AllocatorTest/2.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/2 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.Move 10: [ OK ] AllocatorTest/3.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/3 (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 60 tests from 19 test cases ran. (3 ms total) 10: [ PASSED ] 60 tests. 10/40 Test #10: GpuUtilsUnitTests ................ Passed 0.17 sec test 11 Start 11: HardwareUnitTests 11: Test command: /build/gromacs-2019.1/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 4 tests from 1 test case. 11: [----------] Global test environment set-up. 11: [----------] 4 tests from HardwareTopologyTest 11: [ RUN ] HardwareTopologyTest.Execute 11: [ OK ] HardwareTopologyTest.Execute (9 ms) 11: [ RUN ] HardwareTopologyTest.HwlocExecute 11: [ OK ] HardwareTopologyTest.HwlocExecute (8 ms) 11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (10 ms) 11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (9 ms) 11: [----------] 4 tests from HardwareTopologyTest (36 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 4 tests from 1 test case ran. (36 ms total) 11: [ PASSED ] 4 tests. 11/40 Test #11: HardwareUnitTests ................ Passed 0.21 sec test 12 Start 12: MathUnitTests 12: Test command: /build/gromacs-2019.1/build/basic-dp/bin/math-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 112 tests from 20 test cases. 12: [----------] Global test environment set-up. 12: [----------] 1 test from EmptyArrayRefWithPaddingTest 12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 12: 12: [----------] 6 tests from StructureSimilarityTest 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 12: [----------] 6 tests from StructureSimilarityTest (1 ms total) 12: 12: [----------] 21 tests from FunctionTest 12: [ RUN ] FunctionTest.StaticLog2 12: [ OK ] FunctionTest.StaticLog2 (88 ms) 12: [ RUN ] FunctionTest.Log2I32Bit 12: [ OK ] FunctionTest.Log2I32Bit (46 ms) 12: [ RUN ] FunctionTest.Log2I64Bit 12: [ OK ] FunctionTest.Log2I64Bit (62 ms) 12: [ RUN ] FunctionTest.GreatestCommonDivisor 12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 12: [ RUN ] FunctionTest.InvsqrtFloat 12: [ OK ] FunctionTest.InvsqrtFloat (64 ms) 12: [ RUN ] FunctionTest.InvsqrtDouble 12: [ OK ] FunctionTest.InvsqrtDouble (3 ms) 12: [ RUN ] FunctionTest.InvsqrtInteger 12: [ OK ] FunctionTest.InvsqrtInteger (1 ms) 12: [ RUN ] FunctionTest.InvcbrtFloat 12: [ OK ] FunctionTest.InvcbrtFloat (38 ms) 12: [ RUN ] FunctionTest.InvcbrtDouble 12: [ OK ] FunctionTest.InvcbrtDouble (3 ms) 12: [ RUN ] FunctionTest.InvcbrtInteger 12: [ OK ] FunctionTest.InvcbrtInteger (2 ms) 12: [ RUN ] FunctionTest.SixthrootFloat 12: [ OK ] FunctionTest.SixthrootFloat (40 ms) 12: [ RUN ] FunctionTest.SixthrootDouble 12: [ OK ] FunctionTest.SixthrootDouble (2 ms) 12: [ RUN ] FunctionTest.SixthrootInteger 12: [ OK ] FunctionTest.SixthrootInteger (1 ms) 12: [ RUN ] FunctionTest.InvsixthrootFloat 12: [ OK ] FunctionTest.InvsixthrootFloat (36 ms) 12: [ RUN ] FunctionTest.InvsixthrootDouble 12: [ OK ] FunctionTest.InvsixthrootDouble (17 ms) 12: [ RUN ] FunctionTest.InvsixthrootInteger 12: [ OK ] FunctionTest.InvsixthrootInteger (58 ms) 12: [ RUN ] FunctionTest.Powers 12: [ OK ] FunctionTest.Powers (0 ms) 12: [ RUN ] FunctionTest.ErfInvFloat 12: [ OK ] FunctionTest.ErfInvFloat (60 ms) 12: [ RUN ] FunctionTest.ErfInvDouble 12: [ OK ] FunctionTest.ErfInvDouble (32 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms) 12: [----------] 21 tests from FunctionTest (557 ms total) 12: 12: [----------] 2 tests from InvertMatrixTest 12: [ RUN ] InvertMatrixTest.IdentityIsImpotent 12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertMatrixTest.ComputesInverse 12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 12: [----------] 2 tests from InvertMatrixTest (0 ms total) 12: 12: [----------] 2 tests from InvertBoxMatrixTest 12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanCopyAssign 12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanMoveAssign 12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanSwap 12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanCopyAssign 12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanMoveAssign 12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanSwap 12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanCopyAssign 12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanMoveAssign 12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanSwap 12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanCopyAssign 12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanMoveAssign 12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanSwap 12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanCopyAssign 12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanMoveAssign 12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanSwap 12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanCopyAssign 12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanMoveAssign 12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanSwap 12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (1 ms) 12: [ RUN ] PaddedVectorTest/6.CanCopyAssign 12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanMoveAssign 12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanSwap 12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/6 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanCopyAssign 12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanMoveAssign 12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanSwap 12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanCopyAssign 12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanMoveAssign 12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanSwap 12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanCopyAssign 12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanMoveAssign 12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanSwap 12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 12: 12: [----------] 33 tests from RVecTest 12: [ RUN ] RVecTest.CanBeStoredInVector 12: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAsMutable_rvec 12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Array 12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 12: [ RUN ] RVecTest.CanAddRVecToRvec 12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanAddAssignRVecToRvec 12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractRVecFromRvec 12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanDotProductRVecByRvec 12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanCrossProductRVecByRvec 12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVecInplace 12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 12: [ RUN ] RVecTest.CanScaleRVec 12: [ OK ] RVecTest.CanScaleRVec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVec 12: [ OK ] RVecTest.CanDivideRVec (0 ms) 12: [ RUN ] RVecTest.CanDoUnitvFromRVec 12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanSqLengthOfRVec 12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanLengthOfRVec 12: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToRVec 12: [ OK ] RVecTest.CanCastToRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToDVec 12: [ OK ] RVecTest.CanCastToDVec (0 ms) 12: [ RUN ] RVecTest.CanLeftScalarMultiply 12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanRightScalarMultiply 12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanGetUnitvFromRVec 12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanGetSqLengthOfRVec 12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanGetLengthOfRVec 12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoCrossProductOfRVec 12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoDotProductOfRVec 12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 12: [ RUN ] RVecTest.WorksAs_dvec_Reference 12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_ivec_Reference 12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Reference 12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 12: [ RUN ] RVecTest.CopyConstructorWorks 12: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 12: [ RUN ] RVecTest.CopyAssignmentWorks 12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 12: [ RUN ] RVecTest.MoveConstructorWorks 12: [ OK ] RVecTest.MoveConstructorWorks (1 ms) 12: [ RUN ] RVecTest.MoveAssignmentWorks 12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 12: [----------] 33 tests from RVecTest (1 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 112 tests from 20 test cases ran. (560 ms total) 12: [ PASSED ] 112 tests. 12/40 Test #12: MathUnitTests .................... Passed 0.74 sec test 13 Start 13: MdrunUtilityUnitTests 13: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 17 tests from 1 test case. 13: [----------] Global test environment set-up. 13: [----------] 17 tests from ThreadAffinityTest 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 13: NOTE: Affinity setting failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 13: NOTE: Affinity setting for 1/2 threads failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms) 13: [----------] 17 tests from ThreadAffinityTest (7 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 17 tests from 1 test case ran. (7 ms total) 13: [ PASSED ] 17 tests. 13/40 Test #13: MdrunUtilityUnitTests ............ Passed 0.27 sec test 14 Start 14: MdrunUtilityMpiUnitTests 14: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 13 tests from 2 test cases. 14: [----------] Global test environment set-up. 14: [----------] 6 tests from ThreadAffinityMultiRankTest 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (3 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (2 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (2 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (1 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (1 ms) 14: [----------] 6 tests from ThreadAffinityMultiRankTest (10 ms total) 14: 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (2 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (2 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (2 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (2 ms) 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (11 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 13 tests from 2 test cases ran. (21 ms total) 14: [ PASSED ] 13 tests. 14/40 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.14 sec test 15 Start 15: OnlineHelpUnitTests 15: Test command: /build/gromacs-2019.1/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 22 tests from 4 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from TextTableFormatterTest 15: [ RUN ] TextTableFormatterTest.HandlesBasicCase 15: [ OK ] TextTableFormatterTest.HandlesBasicCase (25 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (41 ms) 15: [ RUN ] TextTableFormatterTest.HandlesIndentation 15: [ OK ] TextTableFormatterTest.HandlesIndentation (25 ms) 15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms) 15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (8 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (9 ms) 15: [----------] 6 tests from TextTableFormatterTest (110 ms total) 15: 15: [----------] 3 tests from HelpManagerTest 15: [ RUN ] HelpManagerTest.HandlesRootTopic 15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 15: [ RUN ] HelpManagerTest.HandlesSubTopics 15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 15: [ RUN ] HelpManagerTest.HandlesInvalidTopics 15: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms) 15: [----------] 3 tests from HelpManagerTest (1 ms total) 15: 15: [----------] 2 tests from HelpTopicFormattingTest 15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms) 15: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 15: 15: [----------] 11 tests from HelpWriterContextTest 15: [ RUN ] HelpWriterContextTest.FormatsParagraphs 15: [ OK ] HelpWriterContextTest.FormatsParagraphs (38 ms) 15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (47 ms) 15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (2 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralText 15: [ OK ] HelpWriterContextTest.FormatsLiteralText (71 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (49 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (3 ms) 15: [ RUN ] HelpWriterContextTest.FormatsBulletList 15: [ OK ] HelpWriterContextTest.FormatsBulletList (51 ms) 15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (19 ms) 15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (22 ms) 15: [ RUN ] HelpWriterContextTest.FormatsGridTable 15: [ OK ] HelpWriterContextTest.FormatsGridTable (2 ms) 15: [ RUN ] HelpWriterContextTest.FormatsTitles 15: [ OK ] HelpWriterContextTest.FormatsTitles (38 ms) 15: [----------] 11 tests from HelpWriterContextTest (342 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 22 tests from 4 test cases ran. (454 ms total) 15: [ PASSED ] 22 tests. 15/40 Test #15: OnlineHelpUnitTests .............. Passed 0.63 sec test 16 Start 16: OptionsUnitTests 16: Test command: /build/gromacs-2019.1/build/basic-dp/bin/options-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 110 tests from 18 test cases. 16: [----------] Global test environment set-up. 16: [----------] 5 tests from AbstractOptionStorageTest 16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms) 16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 16: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 16: 16: [----------] 8 tests from FileNameOptionTest 16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 16: [----------] 8 tests from FileNameOptionTest (0 ms total) 16: 16: [----------] 15 tests from FileNameOptionManagerTest 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 16: 16: [----------] 1 test from OptionsTest 16: [ RUN ] OptionsTest.FailsOnNonsafeStorage 16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 16: [----------] 1 test from OptionsTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerTest 16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (1 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMissingValue 16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesExtraValue 16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesGroups 16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesSections 16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 16: [----------] 9 tests from OptionsAssignerTest (1 ms total) 16: 16: [----------] 4 tests from OptionsAssignerBooleanTest 16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 16: 16: [----------] 13 tests from OptionsAssignerIntegerTest 16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (1 ms) 16: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total) 16: 16: [----------] 5 tests from OptionsAssignerDoubleTest 16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 16: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerStringTest 16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 16: 16: [----------] 6 tests from OptionsAssignerEnumTest 16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 16: 16: [----------] 8 tests from RepeatingOptionSectionTest 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (1 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 16: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total) 16: 16: [----------] 1 test from TimeUnitManagerTest 16: [ RUN ] TimeUnitManagerTest.BasicOperations 16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 16: [----------] 1 test from TimeUnitManagerTest (0 ms total) 16: 16: [----------] 4 tests from TimeUnitBehaviorTest 16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 16: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 16: 16: [----------] 2 tests from TreeValueSupportAssignTest 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (125 ms) 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 16: [----------] 2 tests from TreeValueSupportAssignTest (125 ms total) 16: 16: [----------] 1 test from TreeValueSupportAssignErrorTest 16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (1 ms) 16: [----------] 1 test from TreeValueSupportAssignErrorTest (1 ms total) 16: 16: [----------] 5 tests from TreeValueSupportCheckTest 16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 16: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 16: 16: [----------] 6 tests from TreeValueSupportAdjustTest 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (346 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (80 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms) 16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (3 ms) 16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (139 ms) 16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (2 ms) 16: [----------] 6 tests from TreeValueSupportAdjustTest (571 ms total) 16: 16: [----------] 8 tests from TreeValueSupportTest 16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (93 ms) 16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (2 ms) 16: [ RUN ] TreeValueSupportTest.SupportsInt64Option 16: [ OK ] TreeValueSupportTest.SupportsInt64Option (3 ms) 16: [ RUN ] TreeValueSupportTest.SupportsStringOption 16: [ OK ] TreeValueSupportTest.SupportsStringOption (137 ms) 16: [ RUN ] TreeValueSupportTest.SupportsFloatOption 16: [ OK ] TreeValueSupportTest.SupportsFloatOption (3 ms) 16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (74 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumOption 16: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms) 16: [----------] 8 tests from TreeValueSupportTest (315 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 110 tests from 18 test cases ran. (1017 ms total) 16: [ PASSED ] 110 tests. 16/40 Test #16: OptionsUnitTests ................. Passed 1.54 sec test 17 Start 17: RandomUnitTests 17: Test command: /build/gromacs-2019.1/build/basic-dp/bin/random-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 44 tests from 10 test cases. 17: [----------] Global test environment set-up. 17: [----------] 4 tests from ExponentialDistributionTest 17: [ RUN ] ExponentialDistributionTest.Output 17: [ OK ] ExponentialDistributionTest.Output (104 ms) 17: [ RUN ] ExponentialDistributionTest.Logical 17: [ OK ] ExponentialDistributionTest.Logical (0 ms) 17: [ RUN ] ExponentialDistributionTest.Reset 17: [ OK ] ExponentialDistributionTest.Reset (0 ms) 17: [ RUN ] ExponentialDistributionTest.AltParam 17: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from ExponentialDistributionTest (104 ms total) 17: 17: [----------] 4 tests from GammaDistributionTest 17: [ RUN ] GammaDistributionTest.Output 17: [ OK ] GammaDistributionTest.Output (32 ms) 17: [ RUN ] GammaDistributionTest.Logical 17: [ OK ] GammaDistributionTest.Logical (0 ms) 17: [ RUN ] GammaDistributionTest.Reset 17: [ OK ] GammaDistributionTest.Reset (0 ms) 17: [ RUN ] GammaDistributionTest.AltParam 17: [ OK ] GammaDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from GammaDistributionTest (32 ms total) 17: 17: [----------] 4 tests from NormalDistributionTest 17: [ RUN ] NormalDistributionTest.Output 17: [ OK ] NormalDistributionTest.Output (18 ms) 17: [ RUN ] NormalDistributionTest.Logical 17: [ OK ] NormalDistributionTest.Logical (0 ms) 17: [ RUN ] NormalDistributionTest.Reset 17: [ OK ] NormalDistributionTest.Reset (0 ms) 17: [ RUN ] NormalDistributionTest.AltParam 17: [ OK ] NormalDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from NormalDistributionTest (18 ms total) 17: 17: [----------] 1 test from SeedTest 17: [ RUN ] SeedTest.makeRandomSeed 17: [ OK ] SeedTest.makeRandomSeed (0 ms) 17: [----------] 1 test from SeedTest (0 ms total) 17: 17: [----------] 6 tests from TabulatedNormalDistributionTest 17: [ RUN ] TabulatedNormalDistributionTest.Output14 17: [ OK ] TabulatedNormalDistributionTest.Output14 (58 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Output16 17: [ OK ] TabulatedNormalDistributionTest.Output16 (25 ms) 17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (27 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Logical 17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Reset 17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.AltParam 17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 17: [----------] 6 tests from TabulatedNormalDistributionTest (110 ms total) 17: 17: [----------] 1 test from TabulatedNormalDistributionTableTest 17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (5 ms) 17: [----------] 1 test from TabulatedNormalDistributionTableTest (5 ms total) 17: 17: [----------] 6 tests from ThreeFry2x64Test 17: [ RUN ] ThreeFry2x64Test.Logical 17: [ OK ] ThreeFry2x64Test.Logical (0 ms) 17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 17: [ RUN ] ThreeFry2x64Test.Reseed 17: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 17: [ RUN ] ThreeFry2x64Test.Discard 17: [ OK ] ThreeFry2x64Test.Discard (0 ms) 17: [ RUN ] ThreeFry2x64Test.InvalidCounter 17: [ OK ] ThreeFry2x64Test.InvalidCounter (1 ms) 17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 17: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 17: 17: [----------] 4 tests from UniformIntDistributionTest 17: [ RUN ] UniformIntDistributionTest.Output 17: [ OK ] UniformIntDistributionTest.Output (0 ms) 17: [ RUN ] UniformIntDistributionTest.Logical 17: [ OK ] UniformIntDistributionTest.Logical (0 ms) 17: [ RUN ] UniformIntDistributionTest.Reset 17: [ OK ] UniformIntDistributionTest.Reset (0 ms) 17: [ RUN ] UniformIntDistributionTest.AltParam 17: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 17: 17: [----------] 5 tests from UniformRealDistributionTest 17: [ RUN ] UniformRealDistributionTest.GenerateCanonical 17: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Output 17: [ OK ] UniformRealDistributionTest.Output (0 ms) 17: [ RUN ] UniformRealDistributionTest.Logical 17: [ OK ] UniformRealDistributionTest.Logical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Reset 17: [ OK ] UniformRealDistributionTest.Reset (0 ms) 17: [ RUN ] UniformRealDistributionTest.AltParam 17: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 17: [----------] 5 tests from UniformRealDistributionTest (1 ms total) 17: 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (16 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (25 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (29 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (1 ms) 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (72 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 44 tests from 10 test cases ran. (343 ms total) 17: [ PASSED ] 44 tests. 17/40 Test #17: RandomUnitTests .................. Passed 0.68 sec test 18 Start 18: RestraintTests 18: Test command: /build/gromacs-2019.1/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/RestraintTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 1 test from 1 test case. 18: [----------] Global test environment set-up. 18: [----------] 1 test from RestraintManager 18: [ RUN ] RestraintManager.restraintList 18: [ OK ] RestraintManager.restraintList (0 ms) 18: [----------] 1 test from RestraintManager (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1 test from 1 test case ran. (1 ms total) 18: [ PASSED ] 1 test. 18/40 Test #18: RestraintTests ................... Passed 0.30 sec test 19 Start 19: TableUnitTests 19: Test command: /build/gromacs-2019.1/build/basic-dp/bin/table-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 19: Test timeout computed to be: 30 19: [==========] Running 16 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (5 ms) 19: [ RUN ] SplineTableTest/0.Sinc 19: [ OK ] SplineTableTest/0.Sinc (2 ms) 19: [ RUN ] SplineTableTest/0.LJ12 19: [ OK ] SplineTableTest/0.LJ12 (64 ms) 19: [ RUN ] SplineTableTest/0.PmeCorrection 19: [ OK ] SplineTableTest/0.PmeCorrection (4 ms) 19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (4 ms) 19: [ RUN ] SplineTableTest/0.TwoFunctions 19: [ OK ] SplineTableTest/0.TwoFunctions (129 ms) 19: [ RUN ] SplineTableTest/0.ThreeFunctions 19: [ OK ] SplineTableTest/0.ThreeFunctions (146 ms) 19: [----------] 8 tests from SplineTableTest/0 (355 ms total) 19: 19: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (5 ms) 19: [ RUN ] SplineTableTest/1.Sinc 19: [ OK ] SplineTableTest/1.Sinc (5 ms) 19: [ RUN ] SplineTableTest/1.LJ12 19: [ OK ] SplineTableTest/1.LJ12 (164 ms) 19: [ RUN ] SplineTableTest/1.PmeCorrection 19: [ OK ] SplineTableTest/1.PmeCorrection (5 ms) 19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (3 ms) 19: [ RUN ] SplineTableTest/1.TwoFunctions 19: [ OK ] SplineTableTest/1.TwoFunctions (332 ms) 19: [ RUN ] SplineTableTest/1.ThreeFunctions 19: [ OK ] SplineTableTest/1.ThreeFunctions (376 ms) 19: [----------] 8 tests from SplineTableTest/1 (891 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 16 tests from 2 test cases ran. (1247 ms total) 19: [ PASSED ] 16 tests. 19/40 Test #19: TableUnitTests ................... Passed 1.76 sec test 20 Start 20: TaskAssignmentUnitTests 20: Test command: /build/gromacs-2019.1/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 3 tests from 1 test case. 20: [----------] Global test environment set-up. 20: [----------] 3 tests from GpuIdStringHandlingTest 20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork 20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid 20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow 20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (0 ms) 20: [----------] 3 tests from GpuIdStringHandlingTest (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 3 tests from 1 test case ran. (1 ms total) 20: [ PASSED ] 3 tests. 20/40 Test #20: TaskAssignmentUnitTests .......... Passed 0.12 sec test 21 Start 21: UtilityUnitTests 21: Test command: /build/gromacs-2019.1/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 325 tests from 52 test cases. 21: [----------] Global test environment set-up. 21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.Move 21: [ OK ] AllocatorTest/0.Move (0 ms) 21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/0 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.Move 21: [ OK ] AllocatorTest/1.Move (0 ms) 21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/1 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.Move 21: [ OK ] AllocatorTest/2.Move (0 ms) 21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/2 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.Move 21: [ OK ] AllocatorTest/3.Move (0 ms) 21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/3 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.Move 21: [ OK ] AllocatorTest/4.Move (0 ms) 21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/4 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/5.Move 21: [ OK ] AllocatorTest/5.Move (0 ms) 21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/5 (1 ms total) 21: 21: [----------] 1 test from AllocatorUntypedTest 21: [ RUN ] AllocatorUntypedTest.Comparison 21: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 21: [----------] 1 test from AllocatorUntypedTest (0 ms total) 21: 21: [----------] 1 test from EmptyArrayRefTest 21: [ RUN ] EmptyArrayRefTest.IsEmpty 21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyArrayRefTest (0 ms total) 21: 21: [----------] 1 test from EmptyConstArrayRefTest 21: [ RUN ] EmptyConstArrayRefTest.IsEmpty 21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/4 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (1 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/9 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (1 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/15 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 21: 21: [----------] 4 tests from KeyValueTreeSerializerTest 21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (32 ms) 21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (25 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (25 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (25 ms) 21: [----------] 4 tests from KeyValueTreeSerializerTest (107 ms total) 21: 21: [----------] 6 tests from TreeValueTransformTest 21: [ RUN ] TreeValueTransformTest.SimpleTransforms 21: [ OK ] TreeValueTransformTest.SimpleTransforms (9 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (9 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (8 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromString 21: [ OK ] TreeValueTransformTest.ObjectFromString (3 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (6 ms) 21: [ RUN ] TreeValueTransformTest.ScopedTransformRules 21: [ OK ] TreeValueTransformTest.ScopedTransformRules (21 ms) 21: [----------] 6 tests from TreeValueTransformTest (56 ms total) 21: 21: [----------] 1 test from TreeValueTransformErrorTest 21: [ RUN ] TreeValueTransformErrorTest.ConversionError 21: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 21: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 21: 21: [----------] 2 tests from RegexBasicTest 21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported 21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (1 ms) 21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported 21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (1 ms) 21: [----------] 2 tests from RegexBasicTest (2 ms total) 21: 21: [----------] 5 tests from LoggerTest 21: [ RUN ] LoggerTest.EmptyLoggerWorks 21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToStream 21: [ OK ] LoggerTest.LogsToStream (11 ms) 21: [ RUN ] LoggerTest.LogsToFile 21: [ OK ] LoggerTest.LogsToFile (37 ms) 21: [ RUN ] LoggerTest.LevelFilteringWorks 21: [ OK ] LoggerTest.LevelFilteringWorks (14 ms) 21: [ RUN ] LoggerTest.LogsToMultipleStreams 21: [ OK ] LoggerTest.LogsToMultipleStreams (20 ms) 21: [----------] 5 tests from LoggerTest (82 ms total) 21: 21: [----------] 4 tests from MutexBasicTest 21: [ RUN ] MutexBasicTest.CanBeMade 21: [ OK ] MutexBasicTest.CanBeMade (0 ms) 21: [ RUN ] MutexBasicTest.CanBeLocked 21: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeTryLocked 21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 21: [----------] 4 tests from MutexBasicTest (0 ms total) 21: 21: [----------] 3 tests from MutexTaskTest 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (2 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (3 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 21: [----------] 3 tests from MutexTaskTest (5 ms total) 21: 21: [----------] 4 tests from PathTest 21: [ RUN ] PathTest.StripSourcePrefixWorks 21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks 21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathWorks 21: [ OK ] PathTest.GetParentPathWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathAndBasenameWorks 21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms) 21: [----------] 4 tests from PathTest (0 ms total) 21: 21: [----------] 2 tests from PhysicalNodeCommunicatorTest 21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 21: 21: [----------] 7 tests from StringUtilityTest 21: [ RUN ] StringUtilityTest.StartsWith 21: [ OK ] StringUtilityTest.StartsWith (0 ms) 21: [ RUN ] StringUtilityTest.EndsWith 21: [ OK ] StringUtilityTest.EndsWith (0 ms) 21: [ RUN ] StringUtilityTest.StripSuffixIfPresent 21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 21: [ RUN ] StringUtilityTest.StripString 21: [ OK ] StringUtilityTest.StripString (0 ms) 21: [ RUN ] StringUtilityTest.SplitString 21: [ OK ] StringUtilityTest.SplitString (0 ms) 21: [ RUN ] StringUtilityTest.SplitDelimitedString 21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms) 21: [----------] 7 tests from StringUtilityTest (1 ms total) 21: 21: [----------] 2 tests from FormatStringTest 21: [ RUN ] FormatStringTest.HandlesBasicFormatting 21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 21: [ RUN ] FormatStringTest.HandlesLongStrings 21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 21: [----------] 2 tests from FormatStringTest (0 ms total) 21: 21: [----------] 1 test from StringFormatterTest 21: [ RUN ] StringFormatterTest.HandlesBasicFormatting 21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 21: [----------] 1 test from StringFormatterTest (0 ms total) 21: 21: [----------] 1 test from formatAndJoinTest 21: [ RUN ] formatAndJoinTest.Works 21: [ OK ] formatAndJoinTest.Works (0 ms) 21: [----------] 1 test from formatAndJoinTest (0 ms total) 21: 21: [----------] 1 test from JoinStringsTest 21: [ RUN ] JoinStringsTest.Works 21: [ OK ] JoinStringsTest.Works (0 ms) 21: [----------] 1 test from JoinStringsTest (0 ms total) 21: 21: [----------] 6 tests from ReplaceAllTest 21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesNoMatches 21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 21: [----------] 6 tests from ReplaceAllTest (0 ms total) 21: 21: [----------] 10 tests from TextLineWrapperTest 21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectly 21: [ OK ] TextLineWrapperTest.WrapsCorrectly (20 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (11 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndent 21: [ OK ] TextLineWrapperTest.HandlesIndent (1 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (8 ms) 21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (10 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (1 ms) 21: [----------] 10 tests from TextLineWrapperTest (51 ms total) 21: 21: [----------] 6 tests from TextWriterTest 21: [ RUN ] TextWriterTest.WritesLines 21: [ OK ] TextWriterTest.WritesLines (0 ms) 21: [ RUN ] TextWriterTest.WritesLinesInParts 21: [ OK ] TextWriterTest.WritesLinesInParts (3 ms) 21: [ RUN ] TextWriterTest.WritesWrappedLines 21: [ OK ] TextWriterTest.WritesWrappedLines (1 ms) 21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (1 ms) 21: [ RUN ] TextWriterTest.TracksNewlines 21: [ OK ] TextWriterTest.TracksNewlines (1 ms) 21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (9 ms) 21: [----------] 6 tests from TextWriterTest (15 ms total) 21: 21: [----------] 1 test from TypeTraitsTest 21: [ RUN ] TypeTraitsTest.IsIntegralConstant 21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 21: [----------] 1 test from TypeTraitsTest (0 ms total) 21: 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total) 21: 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (3 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (4 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (4 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (2 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (1 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (14 ms total) 21: 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (1 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 325 tests from 52 test cases ran. (343 ms total) 21: [ PASSED ] 325 tests. 21/40 Test #21: UtilityUnitTests ................. Passed 0.66 sec test 22 Start 22: UtilityMpiUnitTests 22: Test command: /build/gromacs-2019.1/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 2 tests from 1 test case. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from PhysicalNodeCommunicatorTest 22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms) 22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (6 ms) 22: [----------] 2 tests from PhysicalNodeCommunicatorTest (7 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test case ran. (7 ms total) 22: [ PASSED ] 2 tests. 22/40 Test #22: UtilityMpiUnitTests .............. Passed 0.26 sec test 23 Start 23: FileIOTests 23: Test command: /build/gromacs-2019.1/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/FileIOTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 17 tests from 4 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from FileMD5Test 23: [ RUN ] FileMD5Test.CanComputeMD5 23: [ OK ] FileMD5Test.CanComputeMD5 (9 ms) 23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 23: [----------] 2 tests from FileMD5Test (16 ms total) 23: 23: [----------] 9 tests from ReadTest 23: [ RUN ] ReadTest.get_eint_ReadsInteger 23: [ OK ] ReadTest.get_eint_ReadsInteger (23 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_eint64_ReadsInteger 23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsInteger 23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsFloat 23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 23: [ RUN ] ReadTest.get_ereal_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not a 23: real value 23: 23: 23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 23: [----------] 9 tests from ReadTest (24 ms total) 23: 23: [----------] 2 tests from TngTest 23: [ RUN ] TngTest.CanOpenTngFile 23: [ OK ] TngTest.CanOpenTngFile (88 ms) 23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 23: [----------] 2 tests from TngTest (88 ms total) 23: 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (22 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (114 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (138 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 17 tests from 4 test cases ran. (266 ms total) 23: [ PASSED ] 17 tests. 23/40 Test #23: FileIOTests ...................... Passed 0.39 sec test 24 Start 24: PullTest 24: Test command: /build/gromacs-2019.1/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/PullTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 5 tests from 1 test case. 24: [----------] Global test environment set-up. 24: [----------] 5 tests from PullTest 24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (60 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 24: [----------] 5 tests from PullTest (60 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 5 tests from 1 test case ran. (60 ms total) 24: [ PASSED ] 5 tests. 24/40 Test #24: PullTest ......................... Passed 0.43 sec test 25 Start 25: AwhTest 25: Test command: /build/gromacs-2019.1/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/AwhTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 12 tests from 4 test cases. 25: [----------] Global test environment set-up. 25: [----------] 1 test from BiasTest 25: [ RUN ] BiasTest.DetectsCovering 25: [ OK ] BiasTest.DetectsCovering (2 ms) 25: [----------] 1 test from BiasTest (2 ms total) 25: 25: [----------] 1 test from gridTest 25: [ RUN ] gridTest.neighborhood 25: [ OK ] gridTest.neighborhood (3 ms) 25: [----------] 1 test from gridTest (3 ms total) 25: 25: [----------] 8 tests from WithParameters/BiasTest 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (58 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (24 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (27 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (7 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (94 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (60 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (28 ms) 25: [----------] 8 tests from WithParameters/BiasTest (300 ms total) 25: 25: [----------] 2 tests from WithParameters/BiasStateTest 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (65 ms) 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (21 ms) 25: [----------] 2 tests from WithParameters/BiasStateTest (87 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test cases ran. (393 ms total) 25: [ PASSED ] 12 tests. 25/40 Test #25: AwhTest .......................... Passed 0.60 sec test 26 Start 26: SimdUnitTests 26: Test command: /build/gromacs-2019.1/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 26: Test timeout computed to be: 30 26: [==========] Running 86 tests from 3 test cases. 26: [----------] Global test environment set-up. 26: [----------] 41 tests from SimdScalarTest 26: [ RUN ] SimdScalarTest.load 26: [ OK ] SimdScalarTest.load (0 ms) 26: [ RUN ] SimdScalarTest.loadU 26: [ OK ] SimdScalarTest.loadU (0 ms) 26: [ RUN ] SimdScalarTest.store 26: [ OK ] SimdScalarTest.store (0 ms) 26: [ RUN ] SimdScalarTest.storeU 26: [ OK ] SimdScalarTest.storeU (0 ms) 26: [ RUN ] SimdScalarTest.setZero 26: [ OK ] SimdScalarTest.setZero (0 ms) 26: [ RUN ] SimdScalarTest.andNot 26: [ OK ] SimdScalarTest.andNot (0 ms) 26: [ RUN ] SimdScalarTest.fma 26: [ OK ] SimdScalarTest.fma (0 ms) 26: [ RUN ] SimdScalarTest.fms 26: [ OK ] SimdScalarTest.fms (0 ms) 26: [ RUN ] SimdScalarTest.fnma 26: [ OK ] SimdScalarTest.fnma (0 ms) 26: [ RUN ] SimdScalarTest.fnms 26: [ OK ] SimdScalarTest.fnms (0 ms) 26: [ RUN ] SimdScalarTest.maskAdd 26: [ OK ] SimdScalarTest.maskAdd (0 ms) 26: [ RUN ] SimdScalarTest.maskzMul 26: [ OK ] SimdScalarTest.maskzMul (0 ms) 26: [ RUN ] SimdScalarTest.maskzFma 26: [ OK ] SimdScalarTest.maskzFma (0 ms) 26: [ RUN ] SimdScalarTest.abs 26: [ OK ] SimdScalarTest.abs (0 ms) 26: [ RUN ] SimdScalarTest.max 26: [ OK ] SimdScalarTest.max (0 ms) 26: [ RUN ] SimdScalarTest.min 26: [ OK ] SimdScalarTest.min (0 ms) 26: [ RUN ] SimdScalarTest.round 26: [ OK ] SimdScalarTest.round (0 ms) 26: [ RUN ] SimdScalarTest.trunc 26: [ OK ] SimdScalarTest.trunc (0 ms) 26: [ RUN ] SimdScalarTest.reduce 26: [ OK ] SimdScalarTest.reduce (0 ms) 26: [ RUN ] SimdScalarTest.testBits 26: [ OK ] SimdScalarTest.testBits (0 ms) 26: [ RUN ] SimdScalarTest.anyTrue 26: [ OK ] SimdScalarTest.anyTrue (0 ms) 26: [ RUN ] SimdScalarTest.selectByMask 26: [ OK ] SimdScalarTest.selectByMask (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMask 26: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 26: [ RUN ] SimdScalarTest.blend 26: [ OK ] SimdScalarTest.blend (0 ms) 26: [ RUN ] SimdScalarTest.cvtR2I 26: [ OK ] SimdScalarTest.cvtR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvttR2I 26: [ OK ] SimdScalarTest.cvttR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvtI2R 26: [ OK ] SimdScalarTest.cvtI2R (0 ms) 26: [ RUN ] SimdScalarTest.cvtF2D 26: [ OK ] SimdScalarTest.cvtF2D (0 ms) 26: [ RUN ] SimdScalarTest.cvtD2D 26: [ OK ] SimdScalarTest.cvtD2D (0 ms) 26: [ RUN ] SimdScalarTest.loadI 26: [ OK ] SimdScalarTest.loadI (0 ms) 26: [ RUN ] SimdScalarTest.loadUI 26: [ OK ] SimdScalarTest.loadUI (0 ms) 26: [ RUN ] SimdScalarTest.storeI 26: [ OK ] SimdScalarTest.storeI (0 ms) 26: [ RUN ] SimdScalarTest.storeUI 26: [ OK ] SimdScalarTest.storeUI (0 ms) 26: [ RUN ] SimdScalarTest.andNotI 26: [ OK ] SimdScalarTest.andNotI (0 ms) 26: [ RUN ] SimdScalarTest.testBitsI 26: [ OK ] SimdScalarTest.testBitsI (0 ms) 26: [ RUN ] SimdScalarTest.selectByMaskI 26: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMaskI 26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 26: [ RUN ] SimdScalarTest.blendI 26: [ OK ] SimdScalarTest.blendI (0 ms) 26: [ RUN ] SimdScalarTest.cvtB2IB 26: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 26: [ RUN ] SimdScalarTest.cvtIB2B 26: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 26: [ RUN ] SimdScalarTest.expandScalarsToTriplets 26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 26: [----------] 41 tests from SimdScalarTest (1 ms total) 26: 26: [----------] 8 tests from SimdScalarUtilTest 26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 26: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 26: 26: [----------] 37 tests from SimdScalarMathTest 26: [ RUN ] SimdScalarMathTest.copysign 26: [ OK ] SimdScalarMathTest.copysign (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPair 26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 26: [ RUN ] SimdScalarMathTest.inv 26: [ OK ] SimdScalarMathTest.inv (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrt 26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdScalarMathTest.log 26: [ OK ] SimdScalarMathTest.log (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2 26: [ OK ] SimdScalarMathTest.exp2 (0 ms) 26: [ RUN ] SimdScalarMathTest.exp 26: [ OK ] SimdScalarMathTest.exp (0 ms) 26: [ RUN ] SimdScalarMathTest.erf 26: [ OK ] SimdScalarMathTest.erf (0 ms) 26: [ RUN ] SimdScalarMathTest.erfc 26: [ OK ] SimdScalarMathTest.erfc (0 ms) 26: [ RUN ] SimdScalarMathTest.sincos 26: [ OK ] SimdScalarMathTest.sincos (0 ms) 26: [ RUN ] SimdScalarMathTest.sin 26: [ OK ] SimdScalarMathTest.sin (0 ms) 26: [ RUN ] SimdScalarMathTest.cos 26: [ OK ] SimdScalarMathTest.cos (0 ms) 26: [ RUN ] SimdScalarMathTest.tan 26: [ OK ] SimdScalarMathTest.tan (0 ms) 26: [ RUN ] SimdScalarMathTest.asin 26: [ OK ] SimdScalarMathTest.asin (0 ms) 26: [ RUN ] SimdScalarMathTest.acos 26: [ OK ] SimdScalarMathTest.acos (0 ms) 26: [ RUN ] SimdScalarMathTest.atan 26: [ OK ] SimdScalarMathTest.atan (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2 26: [ OK ] SimdScalarMathTest.atan2 (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrection 26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.invSingleAccuracy 26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.logSingleAccuracy 26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.expSingleAccuracy 26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 26: [----------] 37 tests from SimdScalarMathTest (1 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 86 tests from 3 test cases ran. (2 ms total) 26: [ PASSED ] 86 tests. 26/40 Test #26: SimdUnitTests .................... Passed 0.23 sec test 27 Start 27: CompatibilityHelpersTests 27: Test command: /build/gromacs-2019.1/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 6 tests from 6 test cases. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CompatibilityHelper 27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles 27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms) 27: [----------] 1 test from CompatibilityHelper (0 ms total) 27: 27: [----------] 1 test from NotNullConstruction 27: [ RUN ] NotNullConstruction.Works 27: [ OK ] NotNullConstruction.Works (0 ms) 27: [----------] 1 test from NotNullConstruction (0 ms total) 27: 27: [----------] 1 test from NotNullCasting 27: [ RUN ] NotNullCasting.Works 27: [ OK ] NotNullCasting.Works (0 ms) 27: [----------] 1 test from NotNullCasting (0 ms total) 27: 27: [----------] 1 test from NotNullAssignment 27: [ RUN ] NotNullAssignment.Works 27: [ OK ] NotNullAssignment.Works (0 ms) 27: [----------] 1 test from NotNullAssignment (0 ms total) 27: 27: [----------] 1 test from MakeNotNull 27: [ RUN ] MakeNotNull.Works 27: [ OK ] MakeNotNull.Works (0 ms) 27: [----------] 1 test from MakeNotNull (0 ms total) 27: 27: [----------] 1 test from NotNull 27: [ RUN ] NotNull.WorksInContainers 27: [ OK ] NotNull.WorksInContainers (0 ms) 27: [----------] 1 test from NotNull (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 6 tests from 6 test cases ran. (1 ms total) 27: [ PASSED ] 6 tests. 27/40 Test #27: CompatibilityHelpersTests ........ Passed 0.13 sec test 28 Start 28: GmxAnaTest 28: Test command: /build/gromacs-2019.1/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 28: Test timeout computed to be: 600 28: [==========] Running 26 tests from 5 test cases. 28: [----------] Global test environment set-up. 28: [----------] 5 tests from Entropy 28: [ RUN ] Entropy.Schlitter_300_NoLinear 28: [ OK ] Entropy.Schlitter_300_NoLinear (79 ms) 28: [ RUN ] Entropy.Schlitter_300_Linear 28: [ OK ] Entropy.Schlitter_300_Linear (57 ms) 28: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 28: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (22 ms) 28: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 28: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (78 ms) 28: [ RUN ] Entropy.QuasiHarmonic_200_Linear 28: [ OK ] Entropy.QuasiHarmonic_200_Linear (48 ms) 28: [----------] 5 tests from Entropy (284 ms total) 28: 28: [----------] 3 tests from MsdTest 28: [ RUN ] MsdTest.threeDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.threeDimensionalDiffusion (173 ms) 28: [ RUN ] MsdTest.twoDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.twoDimensionalDiffusion (4 ms) 28: [ RUN ] MsdTest.oneDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.oneDimensionalDiffusion (65 ms) 28: [----------] 3 tests from MsdTest (243 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: trr version: GMX_trn_file (single precision) 28: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (91 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (30 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (9 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (20 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (14 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (19 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (183 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (346 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (7 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (7 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (7 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm) 28: -> frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (7 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (7 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (381 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (3 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm) 28: -> frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (11 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 26 tests from 5 test cases ran. (1102 ms total) 28: [ PASSED ] 26 tests. 28/40 Test #28: GmxAnaTest ....................... Passed 1.68 sec test 29 Start 29: GmxPreprocessTests 29: Test command: /build/gromacs-2019.1/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 29: Test timeout computed to be: 30 29: [==========] Running 26 tests from 4 test cases. 29: [----------] Global test environment set-up. 29: [----------] 4 tests from GenconfTest 29: [ RUN ] GenconfTest.nbox_Works 29: [ OK ] GenconfTest.nbox_Works (102 ms) 29: [ RUN ] GenconfTest.nbox_norenumber_Works 29: [ OK ] GenconfTest.nbox_norenumber_Works (36 ms) 29: [ RUN ] GenconfTest.nbox_dist_Works 29: [ OK ] GenconfTest.nbox_dist_Works (28 ms) 29: [ RUN ] GenconfTest.nbox_rot_Works 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: [ OK ] GenconfTest.nbox_rot_Works (26 ms) 29: [----------] 4 tests from GenconfTest (192 ms total) 29: 29: [----------] 5 tests from InsertMoleculesTest 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 8 atoms)! 29: 29: Added 1 molecules (out of 1 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 29: 29: Output configuration contains 8 atoms in 4 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (116 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 2 atoms)! 29: Try 2 success (now 4 atoms)! 29: Try 3 success (now 6 atoms)! 29: Try 4 success (now 8 atoms)! 29: Try 5 success (now 10 atoms)! 29: 29: Added 5 molecules (out of 5 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 29: 29: Output configuration contains 10 atoms in 10 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (39 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 8 atoms)! 29: Try 2 success (now 10 atoms)! 29: 29: Added 2 molecules (out of 2 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 29: 29: Output configuration contains 10 atoms in 4 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (47 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 650 atoms)! 29: Try 2 success (now 652 atoms)! 29: Try 3 success (now 654 atoms)! 29: Try 4 success (now 656 atoms)! 29: 29: Added 4 molecules (out of 4 requested) 29: Replaced 8 residues (24 atoms) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 29: 29: Output configuration contains 632 atoms in 212 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (103 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Read 4 positions from file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 29: 29: Try 1 success (now 2 atoms)! 29: Try 2 success (now 4 atoms)! 29: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 29: Try 13 success (now 6 atoms)! 29: 29: Added 3 molecules (out of 4 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 29: 29: Output configuration contains 6 atoms in 3 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (72 ms) 29: [----------] 5 tests from InsertMoleculesTest (377 ms total) 29: 29: [----------] 12 tests from GetIrTest 29: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp, line 12]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: Ignoring obsolete mdp entry 'title' 29: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 29: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (57 ms) 29: [ RUN ] GetIrTest.HandlesOnlyCutoffScheme 29: [ OK ] GetIrTest.HandlesOnlyCutoffScheme (31 ms) 29: [ RUN ] GetIrTest.UserErrorsSilentlyTolerated 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp, line 5]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.UserErrorsSilentlyTolerated (35 ms) 29: [ RUN ] GetIrTest.DefineHandlesAssignmentOnRhs 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.DefineHandlesAssignmentOnRhs (34 ms) 29: [ RUN ] GetIrTest.EmptyInputWorks 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp, line 1]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.EmptyInputWorks (46 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricField 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricField (42 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldPulsed 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldPulsed (26 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldOscillating 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldOscillating (26 ms) 29: [ RUN ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys 29: [ OK ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys (4 ms) 29: [ RUN ] GetIrTest.ImplicitSolventNoWorks 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ImplicitSolventNoWorks (44 ms) 29: [ RUN ] GetIrTest.ImplicitSolventYesWorks 29: [ OK ] GetIrTest.ImplicitSolventYesWorks (9 ms) 29: [ RUN ] GetIrTest.HandlesMimic 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp, line 3]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.HandlesMimic (26 ms) 29: [----------] 12 tests from GetIrTest (380 ms total) 29: 29: [----------] 5 tests from SolvateTest 29: [ RUN ] SolvateTest.cs_box_Works 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 1x1x1 boxes 29: Solvent box contains 270 atoms in 90 residues 29: Removed 129 solvent atoms due to solvent-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 47 residues 29: Generated solvent containing 141 atoms in 47 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 29: 29: Output configuration contains 141 atoms in 47 residues 29: Volume : 1.331 (nm^3) 29: Density : 1056.36 (g/l) 29: Number of solvent molecules: 47 29: 29: [ OK ] SolvateTest.cs_box_Works (149 ms) 29: [ RUN ] SolvateTest.cs_cp_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 886 residues 29: Generated solvent containing 2658 atoms in 886 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 29: 29: Output configuration contains 2664 atoms in 888 residues 29: Volume : 27.2709 (nm^3) 29: Density : 974.776 (g/l) 29: Number of solvent molecules: 886 29: 29: [ OK ] SolvateTest.cs_cp_Works (120 ms) 29: [ RUN ] SolvateTest.cs_cp_p_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 886 residues 29: Generated solvent containing 2658 atoms in 886 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 29: 29: Output configuration contains 2664 atoms in 888 residues 29: Volume : 27.2709 (nm^3) 29: Density : 974.776 (g/l) 29: Number of solvent molecules: 886 29: 29: Processing topology 29: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works.top) 29: [ OK ] SolvateTest.cs_cp_p_Works (122 ms) 29: [ RUN ] SolvateTest.shell_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 1902 solvent atoms more than 1.000000 nm from solute. 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 252 residues 29: Generated solvent containing 756 atoms in 252 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 29: 29: Output configuration contains 762 atoms in 254 residues 29: Volume : 27.2709 (nm^3) 29: Density : 279.3 (g/l) 29: Number of solvent molecules: 252 29: 29: [ OK ] SolvateTest.shell_Works (71 ms) 29: [ RUN ] SolvateTest.update_Topology_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 3x3x3 boxes 29: Solvent box contains 14952 atoms in 4984 residues 29: Removed 2787 solvent atoms due to solvent-solvent overlap 29: Removed 30 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 2 different molecule types: 29: HOH ( 3 atoms): 1876 residues 29: SOL ( 3 atoms): 2169 residues 29: Generated solvent containing 0 atoms in 0 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 29: 29: Output configuration contains 12141 atoms in 4047 residues 29: Volume : 125 (nm^3) 29: Density : 968.963 (g/l) 29: Number of solvent molecules: 4045 29: 29: Processing topology 29: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 29: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 29: [ OK ] SolvateTest.update_Topology_Works (550 ms) 29: [----------] 5 tests from SolvateTest (1012 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 26 tests from 4 test cases ran. (1961 ms total) 29: [ PASSED ] 26 tests. 29/40 Test #29: GmxPreprocessTests ............... Passed 2.16 sec test 30 Start 30: Pdb2gmxTest 30: Test command: /build/gromacs-2019.1/build/basic-dp/bin/pdb2gmx-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/Pdb2gmxTest.xml" 30: Test timeout computed to be: 480 30: [==========] Running 80 tests from 6 test cases. 30: [----------] Global test environment set-up. 30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (1637 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (1178 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (1073 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (1400 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (1205 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (1368 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (1205 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (1012 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (966 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (1171 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (1298 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (881 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (1024 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (1191 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (1093 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (1071 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (921 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (1073 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (1008 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (1099 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (1231 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (1190 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (1034 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (1029 ms) 30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (27359 ms total) 30: 30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (872 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (888 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (683 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (506 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Marked 37 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 37 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (721 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Marked 53 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 51 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (629 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Marked 36 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 36 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (556 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Marked 33 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 31 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (552 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (540 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (681 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (639 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (500 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Marked 37 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 37 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (649 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Marked 53 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 51 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (726 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Marked 36 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 36 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (597 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Marked 33 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 31 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (513 ms) 30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (10252 ms total) 30: 30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (916 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (646 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (542 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (587 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Marked 39 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 39 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (611 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Marked 57 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 55 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (682 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Marked 38 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 38 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (609 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Marked 35 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 33 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (522 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (533 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (713 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (563 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (639 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Marked 39 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 39 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (565 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Marked 57 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 55 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (676 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Marked 38 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 38 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (591 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Marked 35 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 33 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (521 ms) 30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (9917 ms total) 30: 30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 255, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 691 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 691 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.132 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (1590 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 291, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 788 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 788 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.366 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (1209 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 262, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 727 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 727 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.124 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (1138 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 233, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 634 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 634 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.888 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (1004 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 255, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 691 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 691 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.132 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (1233 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 291, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 788 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 788 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.366 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (1194 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 262, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 727 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 727 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.124 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (1080 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 233, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 634 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 634 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.888 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (1073 ms) 30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (9522 ms total) 30: 30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 663 dihedrals, 48 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.115 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (1635 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 778 dihedrals, 49 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (1088 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 696 dihedrals, 39 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.130 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (1133 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 618 dihedrals, 38 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.885 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (871 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 663 dihedrals, 48 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.115 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (1203 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 778 dihedrals, 49 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (1217 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 696 dihedrals, 39 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.130 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (1145 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 618 dihedrals, 38 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.885 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (958 ms) 30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (9250 ms total) 30: 30: [----------] 8 tests from ChainSep/Pdb2gmxTest 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 258, now 258 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 651 pairs 30: Before cleaning: 661 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 10 cmap torsion pairs 30: There are 661 dihedrals, 46 impropers, 463 angles 30: 648 pairs, 258 bonds and 0 virtual sites 30: Total mass 1882.146 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on changing chain id only (ignoring TER records). 30: 30: Merged chains into joint molecule definitions at 2 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Identified residue PHE6 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Start terminus PHE-6: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 258 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (1029 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 50, now 50 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 123 pairs 30: Before cleaning: 123 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 123 dihedrals, 9 impropers, 88 angles 30: 123 pairs, 50 bonds and 0 virtual sites 30: Total mass 434.421 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 10 donors and 7 acceptors were found. 30: There are 7 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS8 30: NE223 30: MET12 SD55 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 125, now 125 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 317 pairs 30: Before cleaning: 322 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 5 cmap torsion pairs 30: There are 322 dihedrals, 19 impropers, 227 angles 30: 314 pairs, 125 bonds and 0 virtual sites 30: Total mass 846.083 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 258 atoms and 16 residues 30: Total mass in system 1882.146 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on changing chain id only (ignoring TER records). 30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 4 28 30: 2 'B' 7 58 30: 3 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (28 atoms, 4 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 51 atoms 30: Chain time... 30: Processing chain 2 'B' (58 atoms, 7 residues) 30: Identified residue PHE6 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus PHE-6: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 7 residues with 124 atoms 30: Chain time... 30: Processing chain 3 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 51 atoms 4 residues 30: Including chain 2 in system: 124 atoms 7 residues 30: Including chain 3 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (171 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 258, now 258 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 651 pairs 30: Before cleaning: 661 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 10 cmap torsion pairs 30: There are 661 dihedrals, 46 impropers, 463 angles 30: 648 pairs, 258 bonds and 0 virtual sites 30: Total mass 1882.146 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records only (ignoring chain id). 30: 30: Merged chains into joint molecule definitions at 2 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus ILE-9: COO- 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 258 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (946 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 10 donors and 12 acceptors were found. 30: There are 13 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 30: SG9 30: HIS8 NE251 1.055 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 115, now 115 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 288 pairs 30: Before cleaning: 293 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 6 cmap torsion pairs 30: There are 293 dihedrals, 23 impropers, 203 angles 30: 285 pairs, 115 bonds and 0 virtual sites 30: Total mass 888.952 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 60, now 60 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 152 pairs 30: Before cleaning: 152 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 1 cmap torsion pairs 30: There are 152 dihedrals, 5 impropers, 112 angles 30: 152 pairs, 60 bonds and 0 virtual sites 30: Total mass 391.552 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 258 atoms and 16 residues 30: Total mass in system 1882.146 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records only (ignoring chain id). 30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 8 61 30: 2 'B' 3 25 30: 3 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (61 atoms, 8 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus ILE-9: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 8 residues with 114 atoms 30: Chain time... 30: Processing chain 2 'B' (25 atoms, 3 residues) 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 3 residues with 61 atoms 30: Chain time... 30: Processing chain 3 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 114 atoms 8 residues 30: Including chain 2 in system: 61 atoms 3 residues 30: Including chain 3 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (136 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 260, now 260 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 650 pairs 30: Before cleaning: 660 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 8 cmap torsion pairs 30: There are 660 dihedrals, 45 impropers, 466 angles 30: 647 pairs, 260 bonds and 0 virtual sites 30: Total mass 1900.162 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: 30: Merged chains into joint molecule definitions at 3 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Identified residue PHE6 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Start terminus PHE-6: NH3+ 30: End terminus ILE-9: COO- 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 261 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (1006 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 50, now 50 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 123 pairs 30: Before cleaning: 123 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 123 dihedrals, 9 impropers, 88 angles 30: 123 pairs, 50 bonds and 0 virtual sites 30: Total mass 434.421 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 6 donors and 4 acceptors were found. 30: There are 3 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 67, now 67 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 164 pairs 30: Before cleaning: 169 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 169 dihedrals, 13 impropers, 118 angles 30: 161 pairs, 67 bonds and 0 virtual sites 30: Total mass 472.547 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 60, now 60 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 152 pairs 30: Before cleaning: 152 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 1 cmap torsion pairs 30: There are 152 dihedrals, 5 impropers, 112 angles 30: 152 pairs, 60 bonds and 0 virtual sites 30: Total mass 391.552 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 261 atoms and 16 residues 30: Total mass in system 1900.162 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: WARNING: Chain identifier 'B' is used in two non-sequential blocks. 30: They will be treated as separate chains unless you reorder your file. 30: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 4 28 30: 2 'B' 4 33 30: 3 'B' 3 25 30: 4 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (28 atoms, 4 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 51 atoms 30: Chain time... 30: Processing chain 2 'B' (33 atoms, 4 residues) 30: Identified residue PHE6 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Start terminus PHE-6: NH3+ 30: End terminus ILE-9: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 66 atoms 30: Chain time... 30: Processing chain 3 'B' (25 atoms, 3 residues) 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 3 residues with 61 atoms 30: Chain time... 30: Processing chain 4 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 51 atoms 4 residues 30: Including chain 2 in system: 66 atoms 4 residues 30: Including chain 3 in system: 61 atoms 3 residues 30: Including chain 4 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (165 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 256, now 256 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 652 pairs 30: Before cleaning: 662 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 12 cmap torsion pairs 30: There are 662 dihedrals, 47 impropers, 460 angles 30: 649 pairs, 256 bonds and 0 virtual sites 30: Total mass 1864.131 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records and chain id changing. 30: 30: Merged chains into joint molecule definitions at 1 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (1000 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 14 donors and 15 acceptors were found. 30: There are 20 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 173, now 173 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 441 pairs 30: Before cleaning: 446 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 9 cmap torsion pairs 30: There are 446 dihedrals, 29 impropers, 312 angles 30: 438 pairs, 173 bonds and 0 virtual sites 30: Total mass 1262.488 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 255 atoms and 16 residues 30: Total mass in system 1864.131 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records and chain id changing. 30: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 11 86 30: 2 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (86 atoms, 11 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 11 residues with 172 atoms 30: Chain time... 30: Processing chain 2 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 172 atoms 11 residues 30: Including chain 2 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (150 ms) 30: [----------] 8 tests from ChainSep/Pdb2gmxTest (4603 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 80 tests from 6 test cases ran. (70903 ms total) 30: [ PASSED ] 80 tests. 30/40 Test #30: Pdb2gmxTest ...................... Passed 71.37 sec test 31 Start 31: CorrelationsTest 31: Test command: /build/gromacs-2019.1/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 31: Test timeout computed to be: 30 31: [==========] Running 11 tests from 2 test cases. 31: [----------] Global test environment set-up. 31: [----------] 10 tests from AutocorrTest 31: [ RUN ] AutocorrTest.EacNormal 31: [ OK ] AutocorrTest.EacNormal (18 ms) 31: [ RUN ] AutocorrTest.EacNoNormalize 31: [ OK ] AutocorrTest.EacNoNormalize (20 ms) 31: [ RUN ] AutocorrTest.EacCos 31: [ OK ] AutocorrTest.EacCos (39 ms) 31: [ RUN ] AutocorrTest.EacVector 31: [ OK ] AutocorrTest.EacVector (18 ms) 31: [ RUN ] AutocorrTest.EacRcross 31: [ OK ] AutocorrTest.EacRcross (13 ms) 31: [ RUN ] AutocorrTest.EacP0 31: [ OK ] AutocorrTest.EacP0 (29 ms) 31: [ RUN ] AutocorrTest.EacP1 31: [ OK ] AutocorrTest.EacP1 (15 ms) 31: [ RUN ] AutocorrTest.EacP2 31: [ OK ] AutocorrTest.EacP2 (27 ms) 31: [ RUN ] AutocorrTest.EacP3 31: [ OK ] AutocorrTest.EacP3 (31 ms) 31: [ RUN ] AutocorrTest.EacP4 31: [ OK ] AutocorrTest.EacP4 (43 ms) 31: [----------] 10 tests from AutocorrTest (255 ms total) 31: 31: [----------] 1 test from ManyAutocorrelationTest 31: [ RUN ] ManyAutocorrelationTest.Empty 31: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 31: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 11 tests from 2 test cases ran. (303 ms total) 31: [ PASSED ] 11 tests. 31/40 Test #31: CorrelationsTest ................. Passed 0.63 sec test 32 Start 32: AnalysisDataUnitTests 32: Test command: /build/gromacs-2019.1/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 32: Test timeout computed to be: 30 32: [==========] Running 69 tests from 14 test cases. 32: [----------] Global test environment set-up. 32: [----------] 3 tests from AnalysisDataInitializationTest 32: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 32: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 32: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 32: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (11 ms) 32: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 32: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 32: [----------] 3 tests from AnalysisDataInitializationTest (11 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (26 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 32: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/0 (33 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 32: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 32: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/1 (9 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms) 32: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 32: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/2 (11 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms) 32: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 32: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/3 (11 ms total) 32: 32: [----------] 4 tests from AnalysisArrayDataTest 32: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 32: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (2 ms) 32: [ RUN ] AnalysisArrayDataTest.StorageWorks 32: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 32: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 32: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 32: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 32: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 32: [----------] 4 tests from AnalysisArrayDataTest (3 ms total) 32: 32: [----------] 6 tests from AverageModuleTest 32: [ RUN ] AverageModuleTest.BasicTest 32: [ OK ] AverageModuleTest.BasicTest (12 ms) 32: [ RUN ] AverageModuleTest.HandlesMultipointData 32: [ OK ] AverageModuleTest.HandlesMultipointData (26 ms) 32: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 32: [ OK ] AverageModuleTest.HandlesMultipleDataSets (32 ms) 32: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 32: [ OK ] AverageModuleTest.HandlesDataSetAveraging (42 ms) 32: [ RUN ] AverageModuleTest.CanCustomizeXAxis 32: [ OK ] AverageModuleTest.CanCustomizeXAxis (33 ms) 32: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 32: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (31 ms) 32: [----------] 6 tests from AverageModuleTest (176 ms total) 32: 32: [----------] 2 tests from FrameAverageModuleTest 32: [ RUN ] FrameAverageModuleTest.BasicTest 32: [ OK ] FrameAverageModuleTest.BasicTest (17 ms) 32: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 32: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (26 ms) 32: [----------] 2 tests from FrameAverageModuleTest (43 ms total) 32: 32: [----------] 7 tests from AnalysisHistogramSettingsTest 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 32: [----------] 7 tests from AnalysisHistogramSettingsTest (1 ms total) 32: 32: [----------] 2 tests from SimpleHistogramModuleTest 32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (18 ms) 32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (15 ms) 32: [----------] 2 tests from SimpleHistogramModuleTest (33 ms total) 32: 32: [----------] 3 tests from WeightedHistogramModuleTest 32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (42 ms) 32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (9 ms) 32: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 32: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (33 ms) 32: [----------] 3 tests from WeightedHistogramModuleTest (84 ms total) 32: 32: [----------] 3 tests from BinAverageModuleTest 32: [ RUN ] BinAverageModuleTest.ComputesCorrectly 32: [ OK ] BinAverageModuleTest.ComputesCorrectly (41 ms) 32: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 32: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (18 ms) 32: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 32: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (16 ms) 32: [----------] 3 tests from BinAverageModuleTest (75 ms total) 32: 32: [----------] 4 tests from AbstractAverageHistogramTest 32: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 32: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (3 ms) 32: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 32: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (6 ms) 32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (25 ms) 32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (17 ms) 32: [----------] 4 tests from AbstractAverageHistogramTest (51 ms total) 32: 32: [----------] 3 tests from LifetimeModuleTest 32: [ RUN ] LifetimeModuleTest.BasicTest 32: [ OK ] LifetimeModuleTest.BasicTest (8 ms) 32: [ RUN ] LifetimeModuleTest.CumulativeTest 32: [ OK ] LifetimeModuleTest.CumulativeTest (25 ms) 32: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 32: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (38 ms) 32: [----------] 3 tests from LifetimeModuleTest (71 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 69 tests from 14 test cases ran. (612 ms total) 32: [ PASSED ] 69 tests. 32/40 Test #32: AnalysisDataUnitTests ............ Passed 0.93 sec test 33 Start 33: SelectionUnitTests 33: Test command: /build/gromacs-2019.1/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 33: Test timeout computed to be: 30 33: [==========] Running 190 tests from 10 test cases. 33: [----------] Global test environment set-up. 33: [----------] 1 test from IndexGroupTest 33: [ RUN ] IndexGroupTest.RemovesDuplicates 33: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 33: [----------] 1 test from IndexGroupTest (0 ms total) 33: 33: [----------] 15 tests from IndexBlockTest 33: [ RUN ] IndexBlockTest.CreatesUnknownBlock 33: [ OK ] IndexBlockTest.CreatesUnknownBlock (57 ms) 33: [ RUN ] IndexBlockTest.CreatesAtomBlock 33: [ OK ] IndexBlockTest.CreatesAtomBlock (31 ms) 33: [ RUN ] IndexBlockTest.CreatesResidueBlock 33: [ OK ] IndexBlockTest.CreatesResidueBlock (16 ms) 33: [ RUN ] IndexBlockTest.CreatesMoleculeBlock 33: [ OK ] IndexBlockTest.CreatesMoleculeBlock (47 ms) 33: [ RUN ] IndexBlockTest.CreatesResidueBlockWithCompletion 33: [ OK ] IndexBlockTest.CreatesResidueBlockWithCompletion (32 ms) 33: [ RUN ] IndexBlockTest.CreatesMoleculeBlockWithCompletion 33: [ OK ] IndexBlockTest.CreatesMoleculeBlockWithCompletion (170 ms) 33: [ RUN ] IndexBlockTest.CreatesSingleBlock 33: [ OK ] IndexBlockTest.CreatesSingleBlock (57 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 33: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 33: [----------] 15 tests from IndexBlockTest (411 ms total) 33: 33: [----------] 11 tests from IndexMapTest 33: [ RUN ] IndexMapTest.InitializesAtomBlock 33: [ OK ] IndexMapTest.InitializesAtomBlock (52 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 33: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (37 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 33: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (35 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 33: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (46 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 33: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (21 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 33: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (64 ms) 33: [ RUN ] IndexMapTest.InitializesMoleculeBlock 33: [ OK ] IndexMapTest.InitializesMoleculeBlock (41 ms) 33: [ RUN ] IndexMapTest.MapsSingleBlock 33: [ OK ] IndexMapTest.MapsSingleBlock (52 ms) 33: [ RUN ] IndexMapTest.MapsResidueBlocks 33: [ OK ] IndexMapTest.MapsResidueBlocks (53 ms) 33: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 33: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (11 ms) 33: [ RUN ] IndexMapTest.HandlesMultipleRequests 33: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms) 33: [----------] 11 tests from IndexMapTest (415 ms total) 33: 33: [----------] 15 tests from NeighborhoodSearchTest 33: [ RUN ] NeighborhoodSearchTest.SimpleSearch 33: [ OK ] NeighborhoodSearchTest.SimpleSearch (41 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 33: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (46 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchBox 33: [ OK ] NeighborhoodSearchTest.GridSearchBox (8 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 33: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (25 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 33: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (14 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 33: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (6 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 33: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (8 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 33: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 33: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (117 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 33: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 33: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 33: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 33: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 33: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (10 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 33: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (2 ms) 33: [----------] 15 tests from NeighborhoodSearchTest (277 ms total) 33: 33: [----------] 12 tests from PositionCalculationTest 33: [ RUN ] PositionCalculationTest.ComputesAtomPositions 33: [ OK ] PositionCalculationTest.ComputesAtomPositions (31 ms) 33: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 33: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (74 ms) 33: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 33: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (37 ms) 33: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 33: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (78 ms) 33: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 33: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (10 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (38 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionMask 33: [ OK ] PositionCalculationTest.ComputesPositionMask (50 ms) 33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (20 ms) 33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms) 33: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 33: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (19 ms) 33: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 33: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (46 ms) 33: [----------] 12 tests from PositionCalculationTest (405 ms total) 33: 33: [----------] 30 tests from SelectionCollectionTest 33: [ RUN ] SelectionCollectionTest.HandlesNoSelections 33: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 33: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (36 ms) 33: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 33: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 33: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 33: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 33: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (42 ms) 33: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 33: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 33: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions 33: [ OK ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (26 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 33: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 33: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 33: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (1 ms) 33: [----------] 30 tests from SelectionCollectionTest (126 ms total) 33: 33: [----------] 14 tests from SelectionCollectionInteractiveTest 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 33: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (2 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (106 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (59 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (57 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (44 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (39 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 33: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (26 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (31 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (7 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms) 33: [----------] 14 tests from SelectionCollectionInteractiveTest (379 ms total) 33: 33: [----------] 66 tests from SelectionCollectionDataTest 33: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 33: [ OK ] SelectionCollectionDataTest.HandlesAllNone (32 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 33: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (9 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResnr 33: [ OK ] SelectionCollectionDataTest.HandlesResnr (42 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 33: [ OK ] SelectionCollectionDataTest.HandlesResIndex (73 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 33: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (58 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 33: [ OK ] SelectionCollectionDataTest.HandlesAtomname (44 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 33: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (50 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 33: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (41 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesChain 33: [ OK ] SelectionCollectionDataTest.HandlesChain (34 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMass 33: [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesCharge 33: [ OK ] SelectionCollectionDataTest.HandlesCharge (49 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 33: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (25 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 33: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (50 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 33: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (26 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBeta 33: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResname 33: [ OK ] SelectionCollectionDataTest.HandlesResname (27 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (76 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 33: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (99 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 33: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (83 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (23 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (27 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (25 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (97 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (71 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (174 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 33: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (60 ms) 33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (69 ms) 33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (32 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 33: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (30 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 33: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (35 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (40 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (33 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (55 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (40 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (48 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (15 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 33: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (18 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (34 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (16 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 33: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (31 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 33: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (58 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 33: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (35 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 33: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (28 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 33: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (21 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 33: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (33 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 33: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (33 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (75 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (34 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (8 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (27 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 33: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (33 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 33: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (45 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 33: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (12 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 33: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (25 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (3 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 33: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (3 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 33: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (37 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (34 ms) 33: [----------] 66 tests from SelectionCollectionDataTest (2360 ms total) 33: 33: [----------] 17 tests from SelectionOptionTest 33: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 33: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 33: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 33: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms) 33: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 33: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (1 ms) 33: [ RUN ] SelectionOptionTest.ChecksEmptySelections 33: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms) 33: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 33: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooManySelections 33: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 33: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 33: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesAdjuster 33: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 33: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 33: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 33: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 33: [----------] 17 tests from SelectionOptionTest (10 ms total) 33: 33: [----------] 9 tests from SelectionFileOptionTest 33: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 33: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 33: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 33: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 33: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 33: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 33: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 33: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms) 33: [----------] 9 tests from SelectionFileOptionTest (6 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 190 tests from 10 test cases ran. (4389 ms total) 33: [ PASSED ] 190 tests. 33/40 Test #33: SelectionUnitTests ............... Passed 4.71 sec test 34 Start 34: TrajectoryAnalysisUnitTests 34: Test command: /build/gromacs-2019.1/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 34: Test timeout computed to be: 30 34: [==========] Running 74 tests from 14 test cases. 34: [----------] Global test environment set-up. 34: [----------] 5 tests from ClustsizeTest 34: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 34: There is one group in the index 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 24 34: cmid: 2, cmax: 4, max_size: 6 34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (344 ms) 34: [ RUN ] ClustsizeTest.NoMolShortCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 34: There is one group in the index 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 24 34: cmid: 1, cmax: 6, max_size: 6 34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (30 ms) 34: [ RUN ] ClustsizeTest.MolDefaultCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 2, cmax: 4, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (80 ms) 34: [ RUN ] ClustsizeTest.MolShortCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 1, cmax: 6, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (47 ms) 34: [ RUN ] ClustsizeTest.MolCSize 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 2, cmax: 4, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolCSize (42 ms) 34: [----------] 5 tests from ClustsizeTest (543 ms total) 34: 34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (130 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 34: Reading frames from gro file 'Test system', 8 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (34 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 34: Reading frames from gro file 'Test system', 8 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (8 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms) 34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (173 ms total) 34: 34: [----------] 11 tests from AngleModuleTest 34: [ RUN ] AngleModuleTest.ComputesSimpleAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesSimpleAngles (107 ms) 34: [ RUN ] AngleModuleTest.ComputesDihedrals 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesDihedrals (23 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorPairAngles (33 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (51 ms) 34: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (11 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (9 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 34: Reading frames from gro file 'Test system for different angles', 33 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (112 ms) 34: [ RUN ] AngleModuleTest.ComputesMultipleAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesMultipleAngles (56 ms) 34: [ RUN ] AngleModuleTest.HandlesDynamicSelections 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesDynamicSelections (18 ms) 34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (42 ms) 34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (65 ms) 34: [----------] 11 tests from AngleModuleTest (530 ms total) 34: 34: [----------] 3 tests from DistanceModuleTest 34: [ RUN ] DistanceModuleTest.ComputesDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2: 34: Number of samples: 5 34: Average distance: 1.43246 nm 34: Standard deviation: 0.96700 nm 34: [ OK ] DistanceModuleTest.ComputesDistances (14 ms) 34: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2: 34: Number of samples: 5 34: Average distance: 1.43246 nm 34: Standard deviation: 0.96700 nm 34: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 34: Number of samples: 4 34: Average distance: 1.81066 nm 34: Standard deviation: 0.79289 nm 34: [ OK ] DistanceModuleTest.ComputesMultipleDistances (39 ms) 34: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2 and res_cog x < 2.8: 34: Number of samples: 3 34: Average distance: 1.72076 nm 34: Standard deviation: 1.24839 nm 34: [ OK ] DistanceModuleTest.HandlesDynamicSelections (67 ms) 34: [----------] 3 tests from DistanceModuleTest (121 ms total) 34: 34: [----------] 2 tests from FreeVolumeModuleTest 34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for 40 particles. These were set to zero. 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: cutoff = 0.18 nm 34: probe_radius = 0 nm 34: seed = 13 34: ninsert = 1000 probes per nm^3 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 34: van der Spoel and Luciano T. Costa 34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Free volume 38.02 +/- 0.00 % 34: Total volume 68.92 +/- 0.00 nm^3 34: Number of molecules 340 total mass 63491.38 Dalton 34: Average molar mass: 186.74 Dalton 34: Density rho: 1529.71 +/- 0.00 nm^3 34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 34: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 34: Fractional free volume 0.194 +/- 0.000 34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (524 ms) 34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: cutoff = 0.18 nm 34: probe_radius = 0 nm 34: seed = 17 34: ninsert = 1000 probes per nm^3 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 34: van der Spoel and Luciano T. Costa 34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Free volume 38.48 +/- 0.00 % 34: Total volume 68.92 +/- 0.00 nm^3 34: Number of molecules 340 total mass 63491.38 Dalton 34: Average molar mass: 186.74 Dalton 34: Density rho: 1529.71 +/- 0.00 nm^3 34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 34: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 34: Fractional free volume 0.200 +/- 0.000 34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (369 ms) 34: [----------] 2 tests from FreeVolumeModuleTest (893 ms total) 34: 34: [----------] 7 tests from PairDistanceModuleTest 34: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesAllDistances (44 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (57 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (26 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (25 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (65 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (20 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (66 ms) 34: [----------] 7 tests from PairDistanceModuleTest (304 ms total) 34: 34: [----------] 5 tests from RdfModuleTest 34: [ RUN ] RdfModuleTest.BasicTest 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.BasicTest (146 ms) 34: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 34: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (76 ms) 34: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (74 ms) 34: [ RUN ] RdfModuleTest.CalculatesSurf 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.CalculatesSurf (67 ms) 34: [ RUN ] RdfModuleTest.CalculatesXY 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.CalculatesXY (111 ms) 34: [----------] 5 tests from RdfModuleTest (474 ms total) 34: 34: [----------] 5 tests from SasaModuleTest 34: [ RUN ] SasaModuleTest.BasicTest 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.BasicTest (265 ms) 34: [ RUN ] SasaModuleTest.HandlesSelectedResidues 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesSelectedResidues (68 ms) 34: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (41 ms) 34: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (90 ms) 34: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (72 ms) 34: [----------] 5 tests from SasaModuleTest (541 ms total) 34: 34: [----------] 8 tests from SelectModuleTest 34: [ RUN ] SelectModuleTest.BasicTest 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.BasicTest (112 ms) 34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (22 ms) 34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (66 ms) 34: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (17 ms) 34: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (36 ms) 34: [ RUN ] SelectModuleTest.NormalizesSizes 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.NormalizesSizes (54 ms) 34: [ RUN ] SelectModuleTest.WritesResidueNumbers 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.WritesResidueNumbers (13 ms) 34: [ RUN ] SelectModuleTest.WritesResidueIndices 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.WritesResidueIndices (50 ms) 34: [----------] 8 tests from SelectModuleTest (373 ms total) 34: 34: [----------] 10 tests from SurfaceAreaTest 34: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 34: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 34: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 34: [ OK ] SurfaceAreaTest.ComputesTwoPoints (4 ms) 34: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 34: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (4 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints12 34: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints32 34: [ OK ] SurfaceAreaTest.SurfacePoints32 (8 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints42 34: [ OK ] SurfaceAreaTest.SurfacePoints42 (8 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints122 34: [ OK ] SurfaceAreaTest.SurfacePoints122 (10 ms) 34: [ RUN ] SurfaceAreaTest.Computes100Points 34: [ OK ] SurfaceAreaTest.Computes100Points (8 ms) 34: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 34: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (24 ms) 34: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 34: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (23 ms) 34: [----------] 10 tests from SurfaceAreaTest (92 ms total) 34: 34: [----------] 4 tests from TopologyInformation 34: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 34: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 34: [ RUN ] TopologyInformation.WorksWithGroFile 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TopologyInformation.WorksWithGroFile (10 ms) 34: [ RUN ] TopologyInformation.WorksWithPdbFile 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TopologyInformation.WorksWithPdbFile (16 ms) 34: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 34: 34: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp, line 1]: 34: /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 34: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 34: scheme was introduced, but the group scheme was still the default. The 34: default is now the Verlet scheme, so you will observe different behaviour. 34: 34: 34: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: For a correct single-point energy evaluation with nsteps = 0, use 34: continuation = yes to avoid constraining the input coordinates. 34: 34: Setting the LD random seed to 1276853077 34: Generated 330891 of the 330891 non-bonded parameter combinations 34: Generating 1-4 interactions: fudge = 0.5 34: Generated 330891 of the 330891 1-4 parameter combinations 34: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 34: 34: NOTE 3 [file lysozyme.top, line 1465]: 34: System has non-zero total charge: 2.000000 34: Total charge should normally be an integer. See 34: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 34: for discussion on how close it should be to an integer. 34: 34: 34: 34: Removing all charge groups because cutoff-scheme=Verlet 34: Number of degrees of freedom in T-Coupling group rest is 465.00 34: 34: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: NVE simulation with an initial temperature of zero: will use a Verlet 34: buffer of 10%. Check your energy drift! 34: 34: 34: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: You are using a plain Coulomb cut-off, which might produce artifacts. 34: You might want to consider using PME electrostatics. 34: 34: 34: 34: There were 5 notes 34: Reading file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.1 (double precision) 34: Reading file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.1 (double precision) 34: Analysing residue names: 34: There are: 10 Protein residues 34: Analysing Protein... 34: This run will generate roughly 0 Mb of data 34: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (2431 ms) 34: [----------] 4 tests from TopologyInformation (2457 ms total) 34: 34: [----------] 4 tests from TrajectoryModuleTest 34: [ RUN ] TrajectoryModuleTest.BasicTest 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.BasicTest (54 ms) 34: [ RUN ] TrajectoryModuleTest.PlotsXOnly 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.PlotsXOnly (33 ms) 34: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (26 ms) 34: [ RUN ] TrajectoryModuleTest.HandlesNoForces 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.HandlesNoForces (54 ms) 34: [----------] 4 tests from TrajectoryModuleTest (167 ms total) 34: 34: [----------] 5 tests from UnionFinderTest 34: [ RUN ] UnionFinderTest.WorksEmpty 34: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 34: [ RUN ] UnionFinderTest.BasicMerges 34: [ OK ] UnionFinderTest.BasicMerges (1 ms) 34: [ RUN ] UnionFinderTest.LargerMerges 34: [ OK ] UnionFinderTest.LargerMerges (0 ms) 34: [ RUN ] UnionFinderTest.LongRightMerge 34: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 34: [ RUN ] UnionFinderTest.LongLeftMerge 34: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 34: [----------] 5 tests from UnionFinderTest (1 ms total) 34: 34: [----------] 1 test from MappedUnionFinderTest 34: [ RUN ] MappedUnionFinderTest.BasicMerges 34: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 34: [----------] 1 test from MappedUnionFinderTest (0 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 74 tests from 14 test cases ran. (6669 ms total) 34: [ PASSED ] 74 tests. 34/40 Test #34: TrajectoryAnalysisUnitTests ...... Passed 6.93 sec test 35 Start 35: EnergyAnalysisUnitTests 35: Test command: /build/gromacs-2019.1/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 35: Test timeout computed to be: 30 35: [==========] Running 7 tests from 4 test cases. 35: [----------] Global test environment set-up. 35: [----------] 1 test from DhdlTest 35: [ RUN ] DhdlTest.ExtractDhdl 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 35: Reading file /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 35: Note: file tpx version 110, software tpx version 116 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 35: 35: 35: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 35: [ OK ] DhdlTest.ExtractDhdl (353 ms) 35: [----------] 1 test from DhdlTest (354 ms total) 35: 35: [----------] 1 test from OriresTest 35: [ RUN ] OriresTest.ExtractOrires 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 35: Reading file /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 35: Note: file tpx version 111, software tpx version 116 35: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 35: End your selection with 0 35: Selecting all 7 orientation restraints 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 35: [ OK ] OriresTest.ExtractOrires (196 ms) 35: [----------] 1 test from OriresTest (196 ms total) 35: 35: [----------] 3 tests from EnergyTest 35: [ RUN ] EnergyTest.ExtractEnergy 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 35: [ OK ] EnergyTest.ExtractEnergy (78 ms) 35: [ RUN ] EnergyTest.ExtractEnergyByNumber 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 35: Pres. DC -268.49 3 8.52175 13.2804 (bar) 35: [ OK ] EnergyTest.ExtractEnergyByNumber (42 ms) 35: [ RUN ] EnergyTest.ExtractEnergyMixed 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: [ OK ] EnergyTest.ExtractEnergyMixed (42 ms) 35: [----------] 3 tests from EnergyTest (162 ms total) 35: 35: [----------] 2 tests from ViscosityTest 35: [ RUN ] ViscosityTest.EinsteinViscosity 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Pres-XX 20.2092 65 717.193 185.978 (bar) 35: Pres-XY -47.7351 39 372.522 207.456 (bar) 35: Pres-XZ 11.477 31 379.79 6.80818 (bar) 35: Pres-YX -47.7106 39 372.525 207.5 (bar) 35: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 35: Pres-YZ -41.3534 45 401.216 114.663 (bar) 35: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 35: Pres-ZY -41.3119 45 401.196 114.743 (bar) 35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 35: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: [ OK ] ViscosityTest.EinsteinViscosity (26 ms) 35: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Pres-XX 20.2092 65 717.193 185.978 (bar) 35: Pres-XY -47.7351 39 372.522 207.456 (bar) 35: Pres-XZ 11.477 31 379.79 6.80818 (bar) 35: Pres-YX -47.7106 39 372.525 207.5 (bar) 35: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 35: Pres-YZ -41.3534 45 401.216 114.663 (bar) 35: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 35: Pres-ZY -41.3119 45 401.196 114.743 (bar) 35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 35: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: [ OK ] ViscosityTest.EinsteinViscosityIntegral (308 ms) 35: [----------] 2 tests from ViscosityTest (334 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 7 tests from 4 test cases ran. (1046 ms total) 35: [ PASSED ] 7 tests. 35/40 Test #35: EnergyAnalysisUnitTests .......... Passed 1.28 sec test 36 Start 36: ToolUnitTests 36: Test command: /build/gromacs-2019.1/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 36: Test timeout computed to be: 30 36: [==========] Running 4 tests from 1 test case. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from ReportMethodsTest 36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 36: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 36: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 36: [ RUN ] ReportMethodsTest.WritesCorrectInformation 36: 36: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp, line 1]: 36: /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 36: scheme was introduced, but the group scheme was still the default. The 36: default is now the Verlet scheme, so you will observe different behaviour. 36: 36: 36: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: For a correct single-point energy evaluation with nsteps = 0, use 36: continuation = yes to avoid constraining the input coordinates. 36: 36: Setting the LD random seed to -1054322294 36: Generated 330891 of the 330891 non-bonded parameter combinations 36: Generating 1-4 interactions: fudge = 0.5 36: Generated 330891 of the 330891 1-4 parameter combinations 36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 36: 36: NOTE 3 [file lysozyme.top, line 1465]: 36: System has non-zero total charge: 2.000000 36: Total charge should normally be an integer. See 36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 36: for discussion on how close it should be to an integer. 36: 36: 36: 36: Removing all charge groups because cutoff-scheme=Verlet 36: Number of degrees of freedom in T-Coupling group rest is 465.00 36: 36: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: NVE simulation with an initial temperature of zero: will use a Verlet 36: buffer of 10%. Check your energy drift! 36: 36: 36: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: You are using a plain Coulomb cut-off, which might produce artifacts. 36: You might want to consider using PME electrostatics. 36: 36: 36: 36: There were 5 notes 36: Reading file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.tpr, VERSION 2019.1 (double precision) 36: Analysing residue names: 36: There are: 10 Protein residues 36: Analysing Protein... 36: This run will generate roughly 0 Mb of data 36: [ OK ] ReportMethodsTest.WritesCorrectInformation (1100 ms) 36: [ RUN ] ReportMethodsTest.ToolEndToEndTest 36: 36: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp, line 1]: 36: /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 36: scheme was introduced, but the group scheme was still the default. The 36: default is now the Verlet scheme, so you will observe different behaviour. 36: 36: 36: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: For a correct single-point energy evaluation with nsteps = 0, use 36: continuation = yes to avoid constraining the input coordinates. 36: 36: Setting the LD random seed to 858930443 36: Generated 330891 of the 330891 non-bonded parameter combinations 36: Generating 1-4 interactions: fudge = 0.5 36: Generated 330891 of the 330891 1-4 parameter combinations 36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 36: 36: NOTE 3 [file lysozyme.top, line 1465]: 36: System has non-zero total charge: 2.000000 36: Total charge should normally be an integer. See 36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 36: for discussion on how close it should be to an integer. 36: 36: 36: 36: Removing all charge groups because cutoff-scheme=Verlet 36: Number of degrees of freedom in T-Coupling group rest is 465.00 36: 36: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: NVE simulation with an initial temperature of zero: will use a Verlet 36: buffer of 10%. Check your energy drift! 36: 36: 36: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: You are using a plain Coulomb cut-off, which might produce artifacts. 36: You might want to consider using PME electrostatics. 36: 36: 36: 36: There were 5 notes 36: Reading file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.tpr, VERSION 2019.1 (double precision) 36: Analysing residue names: 36: There are: 10 Protein residues 36: Analysing Protein... 36: This run will generate roughly 0 Mb of data 36: section: Methods 36: subsection: Simulation system 36: A system of 1 molecules (156 atoms) was simulated. 36: 36: subsection: Simulation settings 36: A total of 0 ns were simulated with a time step of 1 fs. 36: Neighbor searching was performed every 10 steps. 36: The Cut-off algorithm was used for electrostatic interactions. 36: with a cut-off of 1 nm. 36: A single cut-off of 1.1 nm was used for Van der Waals interactions. 36: [ OK ] ReportMethodsTest.ToolEndToEndTest (827 ms) 36: [----------] 4 tests from ReportMethodsTest (1927 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 4 tests from 1 test case ran. (1927 ms total) 36: [ PASSED ] 4 tests. 36/40 Test #36: ToolUnitTests .................... Passed 2.14 sec test 37 Start 37: MdrunTests 37: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdrunTests.xml" 37: Test timeout computed to be: 600 37: [==========] Running 29 tests from 11 test cases. 37: [----------] Global test environment set-up. 37: [----------] 1 test from GromppTest 37: [ RUN ] GromppTest.EmptyMdpFileWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -2038156148 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 12.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: NVE simulation: will use the initial temperature of 1046.791 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 37: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: [ OK ] GromppTest.EmptyMdpFileWorks (565 ms) 37: [----------] 1 test from GromppTest (566 ms total) 37: 37: [----------] 1 test from ImdTest 37: [ RUN ] ImdTest.ImdCanRun 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]: 37: The Berendsen thermostat does not generate the correct kinetic energy 37: distribution. You might want to consider using the V-rescale thermostat. 37: 37: Setting the LD random seed to 605913068 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Group 'SecondWaterMolecule' with 3 atoms can be activated for interactive molecular dynamics (IMD). 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 50, rlist from 1.121 to 1.344 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: IMD: Enabled. This simulation will accept incoming IMD connections. 37: IMD: You chose a port number < 1. Will automatically assign a free port. 37: IMD: Pulling from IMD remote is enabled (-imdpull). 37: IMD: Turning on IMD - port for incoming requests is 0. 37: IMD: Setting up incoming socket. 37: IMD: Listening for IMD connection on port 53261. 37: IMD: -imdwait not set, starting simulation. 37: starting mdrun 'spc2' 37: 2 steps, 0.0 ps. 37: turning all bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 37: Calculated rlist for 1x1 atom pair-list as 1.134 nm, buffer size 0.134 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.121 nm, buffer size 0.121 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.752 0.376 199.9 37: (ns/day) (hour/ns) 37: Performance: 2.757 8.704 37: [ OK ] ImdTest.ImdCanRun (663 ms) 37: [----------] 1 test from ImdTest (663 ms total) 37: 37: [----------] 2 tests from PmeTest 37: [ RUN ] PmeTest.ReproducesEnergies 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 845617494 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 37: NVE simulation: will use the initial temperature of 1046.791 K for 37: determining the Verlet buffer size 37: 37: Estimate for the relative computational load of the PME mesh part: 1.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 37: The optimal PME mesh load for parallel simulations is below 0.5 37: and for highly parallel simulations between 0.25 and 0.33, 37: for higher performance, increase the cut-off and the PME grid spacing. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: Calculating fourier grid dimensions for X Y Z 37: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.508 0.254 199.9 37: (ns/day) (hour/ns) 37: Performance: 7.136 3.363 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.341 0.170 199.9 37: (ns/day) (hour/ns) 37: Performance: 10.645 2.254 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.408 0.204 199.9 37: (ns/day) (hour/ns) 37: Performance: 8.883 2.702 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (808 ms) 37: [ RUN ] PmeTest.ScalesTheBox 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -315526162 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Searching the wall atom type(s) 37: Number of degrees of freedom in T-Coupling group rest is 13.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: NVE simulation: will use the initial temperature of 966.269 K for 37: determining the Verlet buffer size 37: 37: Estimate for the relative computational load of the PME mesh part: 1.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: The optimal PME mesh load for parallel simulations is below 0.5 37: and for highly parallel simulations between 0.25 and 0.33, 37: for higher performance, increase the cut-off and the PME grid spacing. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 0 steps, 0.0 ps. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.032 0.016 197.8 37: (ns/day) (hour/ns) 37: Performance: 5.325 4.507 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.269 K 37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: Calculating fourier grid dimensions for X Y Z 37: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 37: This run will generate roughly 0 Mb of data 37: [ OK ] PmeTest.ScalesTheBox (155 ms) 37: [----------] 2 tests from PmeTest (963 ms total) 37: 37: [----------] 1 test from CompelTest 37: [ RUN ] CompelTest.SwapCanRun 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 37: The Berendsen thermostat does not generate the correct kinetic energy 37: distribution. You might want to consider using the V-rescale thermostat. 37: 37: Setting the LD random seed to 622880581 37: Generated 330891 of the 330891 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 330891 of the 330891 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein' 37: Excluding 3 bonded neighbours molecule type 'OCT' 37: Excluding 1 bonded neighbours molecule type 'NA' 37: Excluding 1 bonded neighbours molecule type 'CL' 37: Excluding 3 bonded neighbours molecule type 'Protein' 37: Excluding 3 bonded neighbours molecule type 'OCT' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Split0 group 'Ch0' contains 83 atoms. 37: Split1 group 'Ch1' contains 83 atoms. 37: Solvent group 'SOL' contains 11931 atoms. 37: Swap group 'NA+' contains 19 atoms. 37: Swap group 'CL-' contains 19 atoms. 37: Number of degrees of freedom in T-Coupling group System is 27869.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.1 (double precision) 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: SWAP: Determining initial numbers of ions per compartment. 37: SWAP: Setting pointers for checkpoint writing 37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 37: starting mdrun 'Channel_coco in octane membrane' 37: 2 steps, 0.0 ps. 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 37: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 1 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 11 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 3.737 1.869 200.0 37: (ns/day) (hour/ns) 37: Performance: 0.693 34.609 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.1 (double precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: SWAP: Setting pointers for checkpoint writing 37: SWAP: Copying channel fluxes from checkpoint file data 37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 37: starting mdrun 'Channel_coco in octane membrane' 37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 2.950 1.475 200.0 37: (ns/day) (hour/ns) 37: Performance: 0.879 27.317 37: [ OK ] CompelTest.SwapCanRun (4992 ms) 37: [----------] 1 test from CompelTest (4992 ms total) 37: 37: [----------] 6 tests from BondedInteractionsTest 37: [ RUN ] BondedInteractionsTest.NormalBondWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1358119816 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 2 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 13 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 188.7 37: (ns/day) (hour/ns) 37: Performance: 146.183 0.164 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalBondWorks (84 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 2131998109 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 2 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 12 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 188.9 37: (ns/day) (hour/ns) 37: Performance: 147.252 0.163 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedBondWorks (41 ms) 37: [ RUN ] BondedInteractionsTest.NormalAngleWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 1140522746 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 1 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 18 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 189.4 37: (ns/day) (hour/ns) 37: Performance: 139.756 0.172 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalAngleWorks (14 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 814902302 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 1 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 21 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 189.5 37: (ns/day) (hour/ns) 37: Performance: 132.646 0.181 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (35 ms) 37: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1721000295 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 21 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 189.5 37: (ns/day) (hour/ns) 37: Performance: 136.647 0.176 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalDihedralWorks (13 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -14029189 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 20 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 190.1 37: (ns/day) (hour/ns) 37: Performance: 128.780 0.186 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (58 ms) 37: [----------] 6 tests from BondedInteractionsTest (245 ms total) 37: 37: [----------] 2 tests from MdrunTerminationTest 37: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1174146255 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 1, rlist from 1.024 to 1 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 100 steps, 0.1 ps. 37: 37: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.239 0.119 199.8 37: (ns/day) (hour/ns) 37: Performance: 2.171 11.053 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.1 (double precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 37: 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.122 0.061 199.6 37: (ns/day) (hour/ns) 37: Performance: 4.237 5.665 37: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (200 ms) 37: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 1116229840 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 1, rlist from 1.024 to 1 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 100 steps, 0.1 ps. 37: 37: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.243 0.122 199.8 37: (ns/day) (hour/ns) 37: Performance: 2.129 11.271 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.1 (double precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 37: 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 37: Checkpoint file is from part 1, new output files will be suffixed '.part0002'. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.243 0.121 199.9 37: (ns/day) (hour/ns) 37: Performance: 2.136 11.234 37: [ OK ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend (263 ms) 37: [----------] 2 tests from MdrunTerminationTest (463 ms total) 37: 37: [----------] 4 tests from MimicTest 37: [ RUN ] MimicTest.OneQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 130298144 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 35 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.002 0.001 191.6 37: (ns/day) (hour/ns) 37: Performance: 107.215 0.224 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.OneQuantumMol (77 ms) 37: [ RUN ] MimicTest.AllQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 815264971 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 31 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 191.6 37: (ns/day) (hour/ns) 37: Performance: 110.484 0.217 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.AllQuantumMol (40 ms) 37: [ RUN ] MimicTest.TwoQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1239195513 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 34 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 191.8 37: (ns/day) (hour/ns) 37: Performance: 112.021 0.214 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.TwoQuantumMol (17 ms) 37: [ RUN ] MimicTest.BondCuts 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1351129767 37: Generated 2211 of the 2211 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 2211 of the 2211 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 66.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: NVE simulation: will use the initial temperature of 300.368 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/ala.gro' 37: 37: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 25 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.003 0.001 194.5 37: (ns/day) (hour/ns) 37: Performance: 62.729 0.383 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 37: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.BondCuts (216 ms) 37: [----------] 4 tests from MimicTest (350 ms total) 37: 37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 37: Setting the LD random seed to 1879392873 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.335 0.168 199.9 37: (ns/day) (hour/ns) 37: Performance: 1.031 23.287 37: Reading frame 0 time 0.000 37: # Atoms 6 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (181 ms) 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 37: Setting the LD random seed to -1035777125 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.428 0.214 199.9 37: (ns/day) (hour/ns) 37: Performance: 0.807 29.752 37: Reading frame 0 time 0.000 37: # Atoms 6 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (229 ms) 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 37: Setting the LD random seed to 543542788 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.392 0.196 199.9 37: (ns/day) (hour/ns) 37: Performance: 0.880 27.262 37: Reading frame 0 time 0.000 37: # Atoms 3 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (210 ms) 37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (620 ms total) 37: 37: [----------] 3 tests from Checking/InitialConstraintsTest 37: [ RUN ] Checking/InitialConstraintsTest.Works/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1177337445 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.246 0.123 199.8 37: (ns/day) (hour/ns) 37: Performance: 1.403 17.105 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (196 ms) 37: [ RUN ] Checking/InitialConstraintsTest.Works/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -311497115 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.193 0.097 199.7 37: (ns/day) (hour/ns) 37: Performance: 1.787 13.432 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (169 ms) 37: [ RUN ] Checking/InitialConstraintsTest.Works/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: Integrator method md-vv-avek is implemented primarily for validation 37: purposes; for molecular dynamics, you should probably be using md or md-vv 37: 37: Setting the LD random seed to 671722733 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.205 0.103 199.8 37: (ns/day) (hour/ns) 37: Performance: 1.680 14.286 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (176 ms) 37: [----------] 3 tests from Checking/InitialConstraintsTest (542 ms total) 37: 37: [----------] 3 tests from MdrunCanWrite/Trajectories 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1248328120 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.337 0.169 199.8 37: (ns/day) (hour/ns) 37: Performance: 3.586 6.693 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (244 ms) 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1474979301 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.336 0.168 199.8 37: (ns/day) (hour/ns) 37: Performance: 3.598 6.671 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (244 ms) 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1123556993 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.315 0.158 199.8 37: (ns/day) (hour/ns) 37: Performance: 3.831 6.264 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (234 ms) 37: [----------] 3 tests from MdrunCanWrite/Trajectories (722 ms total) 37: 37: [----------] 3 tests from MdrunCanWrite/NptTrajectories 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1041331748 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.279 0.140 199.8 37: (ns/day) (hour/ns) 37: Performance: 1.857 12.927 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (214 ms) 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 645944882 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.268 0.134 199.8 37: (ns/day) (hour/ns) 37: Performance: 1.931 12.430 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (208 ms) 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -2102924498 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: 37: WARNING: Using the slow plain C kernels. This should 37: not happen during routine usage on supported platforms. 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.199 0.100 199.7 37: (ns/day) (hour/ns) 37: Performance: 2.604 9.217 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (173 ms) 37: [----------] 3 tests from MdrunCanWrite/NptTrajectories (595 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 29 tests from 11 test cases ran. (10721 ms total) 37: [ PASSED ] 29 tests. 37/40 Test #37: MdrunTests ....................... Passed 11.20 sec test 38 Start 38: MdrunNonIntegratorTests 38: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 38: Test timeout computed to be: 600 38: [==========] Running 57 tests from 4 test cases. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -4.79910464433648e+01 38: Maximum force = 1.86297359800823e+02 on atom 13 38: Norm of force = 8.77219867200409e+01 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (759 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 3.02331e+02 on atom 3 38: F-Norm = 1.18024e+02 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -5.58622539552396e+01 38: Maximum force = 4.27274823589569e+02 on atom 13 38: Norm of force = 1.84530029788183e+02 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (689 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 22.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 3.19376899489614e+02 38: Maximum force = 9.99884921027275e+03 on atom 9 38: Norm of force = 4.61669565061009e+03 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (506 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: 38: NOTE 3 [file glycine_vacuo.top, line 12]: 38: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 38: 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 22.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 2.41575e+04 on atom 10 38: F-Norm = 1.18451e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.51743017875791e+02 38: Maximum force = 7.42089573427941e+03 on atom 9 38: Norm of force = 3.56929298621805e+03 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (311 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 3 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -1.56984194095142e+02 38: Maximum force = 4.56923625858570e+02 on atom 17 38: Norm of force = 1.83258377483232e+02 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (256 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 3 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: 38: NOTE 4 [file unknown]: 38: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 1.06800e+03 on atom 28 38: F-Norm = 4.26922e+02 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -1.69410778941237e+02 38: Maximum force = 2.18225948179336e+02 on atom 17 38: Norm of force = 7.92068036007829e+01 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (56 ms) 38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2577 ms total) 38: 38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents converged to Fmax < 10 in 1 steps 38: Potential Energy = -9.74257075835450e-01 38: Maximum force = 4.01322929015108e+00 on atom 1 38: Norm of force = 1.63839399694368e+00 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (102 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 4.01323e+00 on atom 1 38: F-Norm = 1.63839e+00 38: 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 38: Potential Energy = -9.90642313893957e-01 38: Maximum force = 2.57812909491105e+00 on atom 1 38: Norm of force = 1.05251679559258e+00 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (25 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: WARNING 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: 38: There was 1 warning 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Low-Memory BFGS Minimizer: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: Using 10 BFGS correction steps. 38: 38: F-max = 4.01323e+00 on atom 1 38: F-Norm = 1.63839e+00 38: 38: 38: writing lowest energy coordinates. 38: 38: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 38: Potential Energy = -9.90642313893957e-01 38: Maximum force = 2.57812909491105e+00 on atom 1 38: Norm of force = 1.05251679559258e+00 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (43 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 3.19395484629890e+02 38: Maximum force = 9.97041707215792e+03 on atom 9 38: Norm of force = 4.62274878672162e+03 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (373 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 2.41672e+04 on atom 10 38: F-Norm = 1.19357e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.56258793634223e+02 38: Maximum force = 7.50181017498406e+03 on atom 9 38: Norm of force = 3.61390332570589e+03 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (322 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: WARNING 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: 38: There was 1 warning 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: 38: Low-Memory BFGS Minimizer: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: Using 10 BFGS correction steps. 38: 38: F-max = 2.41672e+04 on atom 10 38: F-Norm = 1.19357e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.84722734378543e+03 38: Maximum force = 2.12615356182373e+04 on atom 9 38: Norm of force = 1.01988549359680e+04 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (334 ms) 38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1199 ms total) 38: 38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: NVE simulation: will use the initial temperature of 68.810 K for 38: determining the Verlet buffer size 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.399 0.200 199.9 38: (ns/day) (hour/ns) 38: Performance: 7.350 3.266 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.trr' 38: 38: trr version: GMX_trn_file (double precision) 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 195.0 38: (ns/day) (hour/ns) 38: Performance: 944.587 0.025 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (246 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: NVE simulation: will use the initial temperature of 68.810 K for 38: determining the Verlet buffer size 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.407 0.204 199.9 38: (ns/day) (hour/ns) 38: Performance: 7.214 3.327 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 194.8 38: (ns/day) (hour/ns) 38: Performance: 890.774 0.027 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (247 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 38: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.352 0.176 199.9 38: (ns/day) (hour/ns) 38: Performance: 8.339 2.878 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 26 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 195.3 38: (ns/day) (hour/ns) 38: Performance: 883.493 0.027 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (225 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.736 0.368 199.9 38: (ns/day) (hour/ns) 38: Performance: 3.992 6.012 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 25 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 195.2 38: (ns/day) (hour/ns) 38: Performance: 863.191 0.028 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (412 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: NVE simulation: will use the initial temperature of 398.997 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.439 0.220 199.9 38: (ns/day) (hour/ns) 38: Performance: 6.685 3.590 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 15 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 194.9 38: (ns/day) (hour/ns) 38: Performance: 921.555 0.026 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (937 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: NVE simulation: will use the initial temperature of 398.997 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.333 0.167 199.8 38: (ns/day) (hour/ns) 38: Performance: 8.819 2.721 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 16 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 195.0 38: (ns/day) (hour/ns) 38: Performance: 808.371 0.030 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (925 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.401 0.201 199.9 38: (ns/day) (hour/ns) 38: Performance: 7.315 3.281 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 22 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 195.5 38: (ns/day) (hour/ns) 38: Performance: 829.486 0.029 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (928 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.445 0.223 199.9 38: (ns/day) (hour/ns) 38: Performance: 6.594 3.640 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 195.4 38: (ns/day) (hour/ns) 38: Performance: 852.088 0.028 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (965 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: NVE simulation: will use the initial temperature of 456.887 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 7 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 7 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.303 0.152 199.8 38: (ns/day) (hour/ns) 38: Performance: 9.684 2.478 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 197.0 38: (ns/day) (hour/ns) 38: Performance: 474.951 0.051 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (257 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: NVE simulation: will use the initial temperature of 456.887 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 7 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 7 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.302 0.151 199.8 38: (ns/day) (hour/ns) 38: Performance: 9.724 2.468 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.003 196.9 38: (ns/day) (hour/ns) 38: Performance: 426.841 0.056 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (244 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 6 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.360 0.180 199.8 38: (ns/day) (hour/ns) 38: Performance: 8.153 2.944 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 197.0 38: (ns/day) (hour/ns) 38: Performance: 467.243 0.051 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (361 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 6 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.362 0.181 199.8 38: (ns/day) (hour/ns) 38: Performance: 8.108 2.960 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 19 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 197.1 38: (ns/day) (hour/ns) 38: Performance: 456.814 0.053 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (343 ms) 38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (6090 ms total) 38: 38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.549 0.275 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.350 4.486 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 188.7 38: (ns/day) (hour/ns) 38: Performance: 347.997 0.069 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (644 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.556 0.278 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.281 4.545 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 183.5 38: (ns/day) (hour/ns) 38: Performance: 314.734 0.076 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (394 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.642 0.321 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.575 5.246 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 15 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 191.4 38: (ns/day) (hour/ns) 38: Performance: 340.082 0.071 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (429 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.558 0.279 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.259 4.563 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 187.6 38: (ns/day) (hour/ns) 38: Performance: 342.027 0.070 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (387 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.650 0.325 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.515 5.316 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 189.4 38: (ns/day) (hour/ns) 38: Performance: 319.185 0.075 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (419 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.518 0.259 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.665 4.237 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 190.1 38: (ns/day) (hour/ns) 38: Performance: 345.887 0.069 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (364 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.521 0.260 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.639 4.256 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 190.2 38: (ns/day) (hour/ns) 38: Performance: 336.204 0.071 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (352 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.482 0.241 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.084 3.945 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 189.6 38: (ns/day) (hour/ns) 38: Performance: 352.598 0.068 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (336 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.549 0.275 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.344 4.491 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 188.1 38: (ns/day) (hour/ns) 38: Performance: 343.515 0.070 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (381 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.563 0.282 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.211 4.606 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 11 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 192.9 38: (ns/day) (hour/ns) 38: Performance: 297.915 0.081 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (375 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.494 0.247 199.8 38: (ns/day) (hour/ns) 38: Performance: 5.940 4.041 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 189.3 38: (ns/day) (hour/ns) 38: Performance: 315.701 0.076 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (341 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 1.179 0.590 199.9 38: (ns/day) (hour/ns) 38: Performance: 2.492 9.632 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 190.1 38: (ns/day) (hour/ns) 38: Performance: 344.803 0.070 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (691 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.637 0.319 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.607 5.209 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 12 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 190.0 38: (ns/day) (hour/ns) 38: Performance: 299.189 0.080 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (425 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.474 0.237 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.186 3.880 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 15 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 191.5 38: (ns/day) (hour/ns) 38: Performance: 323.850 0.074 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (333 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.489 0.245 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.005 3.996 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 190.6 38: (ns/day) (hour/ns) 38: Performance: 347.761 0.069 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (351 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.530 0.265 199.8 38: (ns/day) (hour/ns) 38: Performance: 5.543 4.330 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 15 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 189.6 38: (ns/day) (hour/ns) 38: Performance: 342.827 0.070 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (360 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.532 0.266 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.521 4.347 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 189.2 38: (ns/day) (hour/ns) 38: Performance: 346.004 0.069 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (364 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.505 0.253 199.8 38: (ns/day) (hour/ns) 38: Performance: 5.817 4.126 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 189.7 38: (ns/day) (hour/ns) 38: Performance: 315.039 0.076 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (351 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.583 0.292 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.034 4.768 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 11 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 193.1 38: (ns/day) (hour/ns) 38: Performance: 285.927 0.084 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (392 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.512 0.256 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.729 4.190 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 188.3 38: (ns/day) (hour/ns) 38: Performance: 347.134 0.069 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (349 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.471 0.236 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.233 3.850 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 11 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 189.3 38: (ns/day) (hour/ns) 38: Performance: 286.339 0.084 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (330 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.981 0.490 199.9 38: (ns/day) (hour/ns) 38: Performance: 2.995 8.014 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 12 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.004 189.4 38: (ns/day) (hour/ns) 38: Performance: 327.047 0.073 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (584 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.610 0.305 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.813 4.986 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 191.8 38: (ns/day) (hour/ns) 38: Performance: 346.783 0.069 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (463 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.452 0.226 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.494 3.695 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 15 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 188.7 38: (ns/day) (hour/ns) 38: Performance: 335.088 0.072 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (384 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.928 0.464 199.9 38: (ns/day) (hour/ns) 38: Performance: 3.165 7.584 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.014 56.6 38: (ns/day) (hour/ns) 38: Performance: 102.061 0.235 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (701 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 1.587 0.794 199.9 38: (ns/day) (hour/ns) 38: Performance: 1.850 12.973 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 190.3 38: (ns/day) (hour/ns) 38: Performance: 348.785 0.069 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (972 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.615 0.307 199.9 38: (ns/day) (hour/ns) 38: Performance: 4.777 5.024 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 188.9 38: (ns/day) (hour/ns) 38: Performance: 343.783 0.070 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (467 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.556 0.278 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.278 4.547 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 189.9 38: (ns/day) (hour/ns) 38: Performance: 315.330 0.076 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (439 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.559 0.280 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.252 4.570 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 189.9 38: (ns/day) (hour/ns) 38: Performance: 316.528 0.076 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (461 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.469 0.235 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.253 3.838 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 23 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 190.2 38: (ns/day) (hour/ns) 38: Performance: 278.899 0.086 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (411 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.483 0.242 199.8 38: (ns/day) (hour/ns) 38: Performance: 6.075 3.951 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 13 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 189.6 38: (ns/day) (hour/ns) 38: Performance: 303.403 0.079 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (409 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.958 0.479 199.9 38: (ns/day) (hour/ns) 38: Performance: 3.065 7.831 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 190.6 38: (ns/day) (hour/ns) 38: Performance: 344.552 0.070 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (650 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.562 0.281 199.9 38: (ns/day) (hour/ns) 38: Performance: 5.219 4.599 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: WARNING: Using the slow plain C kernels. This should 38: not happen during routine usage on supported platforms. 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 14 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 189.6 38: (ns/day) (hour/ns) 38: Performance: 311.724 0.077 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (442 ms) 38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (14753 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 57 tests from 4 test cases ran. (24619 ms total) 38: [ PASSED ] 57 tests. 38/40 Test #38: MdrunNonIntegratorTests .......... Passed 24.88 sec test 39 Start 39: LegacyGroupSchemeMdrunTests 39: Test command: /build/gromacs-2019.1/build/basic-dp/bin/legacy-mdrun-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/LegacyGroupSchemeMdrunTests.xml" 39: Test timeout computed to be: 600 39: [==========] Running 2 tests from 1 test case. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from Simple/TpiTest 39: [ RUN ] Simple/TpiTest.ReproducesOutput/0 39: 39: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0_input.mdp]: 39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be 39: removed in a future release when all interaction forms are supported for 39: the verlet scheme. The verlet scheme already scales better, and it is 39: compatible with GPUs and other accelerators. 39: 39: Generated 331705 of the 331705 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 331705 of the 331705 1-4 parameter combinations 39: Excluding 2 bonded neighbours molecule type 'SOL' 39: Excluding 3 bonded neighbours molecule type 'methane' 39: Number of degrees of freedom in T-Coupling group System is 1308.00 39: 39: There was 1 note 39: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2019.1 (double precision) 39: Using 1 MPI thread 39: 39: 39: NOTE: Thread affinity was not set. 39: 39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be 39: removed in a future release when 'verlet' supports all interaction forms. 39: 39: Reading frames from gro file '216 water molecules', 648 atoms. 39: Reading frame 0 time 0.000 mu 8.698e+02 8.698e+02 39: Last frame 0 time 0.000 39: Analysing residue names: 39: There are: 216 Water residues 39: There are: 1 Other residues 39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm 39: Largest charge group radii for Coulomb: 0.100, 0.100 nm 39: This run will generate roughly 0 Mb of data 39: [ OK ] Simple/TpiTest.ReproducesOutput/0 (839 ms) 39: [ RUN ] Simple/TpiTest.ReproducesOutput/1 39: 39: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1_input.mdp]: 39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be 39: removed in a future release when all interaction forms are supported for 39: the verlet scheme. The verlet scheme already scales better, and it is 39: compatible with GPUs and other accelerators. 39: 39: Generated 331705 of the 331705 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 331705 of the 331705 1-4 parameter combinations 39: Excluding 2 bonded neighbours molecule type 'SOL' 39: Excluding 3 bonded neighbours molecule type 'methane' 39: Number of degrees of freedom in T-Coupling group System is 1308.00 39: 39: There was 1 note 39: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2019.1 (double precision) 39: Using 1 MPI thread 39: 39: 39: NOTE: Thread affinity was not set. 39: 39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be 39: removed in a future release when 'verlet' supports all interaction forms. 39: 39: Reading frames from gro file '216 water molecules', 648 atoms. 39: Reading frame 0 time 0.000 mu 9.151e+01 9.151e+01 39: Last frame 0 time 0.000 39: Analysing residue names: 39: There are: 216 Water residues 39: There are: 1 Other residues 39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm 39: Largest charge group radii for Coulomb: 0.100, 0.100 nm 39: This run will generate roughly 0 Mb of data 39: [ OK ] Simple/TpiTest.ReproducesOutput/1 (824 ms) 39: [----------] 2 tests from Simple/TpiTest (1663 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 2 tests from 1 test case ran. (1664 ms total) 39: [ PASSED ] 2 tests. 39/40 Test #39: LegacyGroupSchemeMdrunTests ...... Passed 1.79 sec test 40 Start 40: MdrunMpiTests 40: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 40: Test timeout computed to be: 600 40: [==========] Running 21 tests from 7 test cases. 40: [----------] Global test environment set-up. 40: [----------] 1 test from DomainDecompositionSpecialCasesTest 40: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to -501481316 40: Generated 3 of the 3 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 3 of the 3 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 9.00 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting mdrun 'spc2' 40: 0 steps, 0.0 ps. 40: 40: NOTE: 43 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.001 0.001 170.5 40: (ns/day) (hour/ns) 40: Performance: 120.115 0.200 40: This run will generate roughly 0 Mb of data 40: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (38 ms) 40: [----------] 1 test from DomainDecompositionSpecialCasesTest (38 ms total) 40: 40: [----------] 4 tests from MimicTest 40: [ RUN ] MimicTest.OneQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to -709911574 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 36 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.002 0.001 192.3 40: (ns/day) (hour/ns) 40: Performance: 104.284 0.230 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.OneQuantumMol (25 ms) 40: [ RUN ] MimicTest.AllQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 475194721 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 36 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.002 0.001 191.7 40: (ns/day) (hour/ns) 40: Performance: 103.215 0.233 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.AllQuantumMol (23 ms) 40: [ RUN ] MimicTest.TwoQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 1665391692 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 34 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.002 0.001 192.1 40: (ns/day) (hour/ns) 40: Performance: 103.480 0.232 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.TwoQuantumMol (25 ms) 40: [ RUN ] MimicTest.BondCuts 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 757264615 40: Generated 2211 of the 2211 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2211 of the 2211 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 66.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: NVE simulation: will use the initial temperature of 300.368 K for 40: determining the Verlet buffer size 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/ala.gro' 40: 40: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 23 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.003 0.001 194.3 40: (ns/day) (hour/ns) 40: Performance: 63.002 0.381 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 40: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.BondCuts (56 ms) 40: [----------] 4 tests from MimicTest (129 ms total) 40: 40: [----------] 1 test from MultiSimTerminationTest 40: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 40: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 40: [----------] 1 test from MultiSimTerminationTest (0 ms total) 40: 40: [----------] 2 tests from PmeTest 40: [ RUN ] PmeTest.ReproducesEnergies 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: Setting the LD random seed to 1727679384 40: Generated 279 of the 1225 non-bonded parameter combinations 40: Excluding 2 bonded neighbours molecule type 'Methanol' 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 12.00 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 40: NVE simulation: will use the initial temperature of 1046.791 K for 40: determining the Verlet buffer size 40: 40: Estimate for the relative computational load of the PME mesh part: 1.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 40: The optimal PME mesh load for parallel simulations is below 0.5 40: and for highly parallel simulations between 0.25 and 0.33, 40: for higher performance, increase the cut-off and the PME grid spacing. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: Calculating fourier grid dimensions for X Y Z 40: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 40: This run will generate roughly 0 Mb of data 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.376 0.188 199.9 40: (ns/day) (hour/ns) 40: Performance: 9.633 2.492 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.407 0.204 199.9 40: (ns/day) (hour/ns) 40: Performance: 8.902 2.696 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.372 0.186 199.9 40: (ns/day) (hour/ns) 40: Performance: 9.749 2.462 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (754 ms) 40: [ RUN ] PmeTest.ScalesTheBox 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 2082803884 40: Generated 279 of the 1225 non-bonded parameter combinations 40: Excluding 2 bonded neighbours molecule type 'Methanol' 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Searching the wall atom type(s) 40: Number of degrees of freedom in T-Coupling group rest is 13.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: NVE simulation: will use the initial temperature of 966.269 K for 40: determining the Verlet buffer size 40: 40: Estimate for the relative computational load of the PME mesh part: 1.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: The optimal PME mesh load for parallel simulations is below 0.5 40: and for highly parallel simulations between 0.25 and 0.33, 40: for higher performance, increase the cut-off and the PME grid spacing. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: starting mdrun 'spc-and-methanol' 40: 0 steps, 0.0 ps. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.032 0.016 197.7 40: (ns/day) (hour/ns) 40: Performance: 5.372 4.468 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.269 K 40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: Calculating fourier grid dimensions for X Y Z 40: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 40: This run will generate roughly 0 Mb of data 40: [ OK ] PmeTest.ScalesTheBox (142 ms) 40: [----------] 2 tests from PmeTest (897 ms total) 40: 40: [----------] 1 test from ReplicaExchangeTerminationTest 40: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 40: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 40: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total) 40: 40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 330891 of the 330891 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 330891 of the 330891 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -4.79910464433648e+01 40: Maximum force = 1.86297359800823e+02 on atom 13 40: Norm of force = 8.77219867200409e+01 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (701 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 330891 of the 330891 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 330891 of the 330891 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 3.02331e+02 on atom 3 40: F-Norm = 1.18024e+02 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -5.58622539552396e+01 40: Maximum force = 4.27274823589569e+02 on atom 13 40: Norm of force = 1.84530029788183e+02 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (705 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 22.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 3.19376899489614e+02 40: Maximum force = 9.99884921027275e+03 on atom 9 40: Norm of force = 4.61669565061009e+03 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 turning H bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (293 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: 40: NOTE 3 [file glycine_vacuo.top, line 12]: 40: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 40: 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 22.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 2.41575e+04 on atom 10 40: F-Norm = 1.18451e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.51743017875791e+02 40: Maximum force = 7.42089573427941e+03 on atom 9 40: Norm of force = 3.56929298621805e+03 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning H bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (297 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 2145 of the 2145 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2145 of the 2145 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 40: 40: NOTE 3 [file unknown]: 40: You are using constraints on all bonds, whereas the forcefield has been 40: parametrized only with constraints involving hydrogen atoms. We suggest 40: using constraints = h-bonds instead, this will also improve performance. 40: 40: Cleaning up constraints and constant bonded interactions with virtual sites 40: Removed 18 Angles with virtual sites, 21 left 40: Removed 10 Proper Dih.s with virtual sites, 44 left 40: Converted 15 Constraints with virtual sites to connections, 7 left 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 23.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -1.56984194095142e+02 40: Maximum force = 4.56923625858570e+02 on atom 17 40: Norm of force = 1.83258377483232e+02 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 turning all bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (42 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 2145 of the 2145 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2145 of the 2145 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 40: 40: NOTE 3 [file unknown]: 40: You are using constraints on all bonds, whereas the forcefield has been 40: parametrized only with constraints involving hydrogen atoms. We suggest 40: using constraints = h-bonds instead, this will also improve performance. 40: 40: 40: NOTE 4 [file unknown]: 40: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 40: 40: Cleaning up constraints and constant bonded interactions with virtual sites 40: Removed 18 Angles with virtual sites, 21 left 40: Removed 10 Proper Dih.s with virtual sites, 44 left 40: Converted 15 Constraints with virtual sites to connections, 7 left 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 23.00 40: 40: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 5 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 1.06800e+03 on atom 28 40: F-Norm = 4.26922e+02 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -1.69410778941237e+02 40: Maximum force = 2.18225948179336e+02 on atom 17 40: Norm of force = 7.92068036007829e+01 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 turning all bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (43 ms) 40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2081 ms total) 40: 40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents converged to Fmax < 10 in 1 steps 40: Potential Energy = -9.74257075835450e-01 40: Maximum force = 4.01322929015108e+00 on atom 1 40: Norm of force = 1.63839399694368e+00 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (14 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 4.01323e+00 on atom 1 40: F-Norm = 1.63839e+00 40: 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 40: Potential Energy = -9.90642313893957e-01 40: Maximum force = 2.57812909491105e+00 on atom 1 40: Norm of force = 1.05251679559258e+00 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (14 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: 40: WARNING 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: 40: There was 1 warning 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 40: 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Low-Memory BFGS Minimizer: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: Using 10 BFGS correction steps. 40: 40: F-max = 4.01323e+00 on atom 1 40: F-Norm = 1.63839e+00 40: 40: 40: writing lowest energy coordinates. 40: 40: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 40: Potential Energy = -9.90642313893957e-01 40: Maximum force = 2.57812909491105e+00 on atom 1 40: Norm of force = 1.05251679559258e+00 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (20 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 3.19395484629890e+02 40: Maximum force = 9.97041707215792e+03 on atom 9 40: Norm of force = 4.62274878672162e+03 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (295 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 2.41672e+04 on atom 10 40: F-Norm = 1.19357e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.56258793634223e+02 40: Maximum force = 7.50181017498406e+03 on atom 9 40: Norm of force = 3.61390332570589e+03 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (296 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: 40: WARNING 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: 40: There was 1 warning 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 40: 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: WARNING: Using the slow plain C kernels. This should 40: not happen during routine usage on supported platforms. 40: 40: Low-Memory BFGS Minimizer: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: Using 10 BFGS correction steps. 40: 40: F-max = 2.41672e+04 on atom 10 40: F-Norm = 1.19357e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.84722734378543e+03 40: Maximum force = 2.12615356182373e+04 on atom 9 40: Norm of force = 1.01988549359680e+04 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (302 ms) 40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (941 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 21 tests from 7 test cases ran. (4086 ms total) 40: [ PASSED ] 21 tests. 40: 40: YOU HAVE 4 DISABLED TESTS 40: 40/40 Test #40: MdrunMpiTests .................... Passed 4.13 sec 100% tests passed, 0 tests failed out of 40 Label Time Summary: GTest = 155.00 sec*proc (40 tests) IntegrationTest = 43.69 sec*proc (5 tests) MpiTest = 0.54 sec*proc (3 tests) SlowTest = 71.37 sec*proc (1 test) UnitTest = 39.94 sec*proc (34 tests) Total Test time (real) = 158.14 sec touch build-basic dh_testdir /usr/bin/make -j3 -C build/mpich make[1]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich/CMakeFiles /build/gromacs-2019.1/build/mpich/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 1%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 2%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/programs /build/gromacs-2019.1/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 2%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 5%] Built target tng_io_obj cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/mpich/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/filenm.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/pargs.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/shellcompletions.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/viewit.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/atomdistribution.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/box.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/cellsizes.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_constraints.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_setup.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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-DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dump.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/ga2la.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp 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-I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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-I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/3dtransforms.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/do_fit.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/functions.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/invertmatrix.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/units.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/utilities.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/veccompare.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/vecdump.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/df_history.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/iforceprovider.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/inputrec.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/md_enums.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/observableshistory.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpformat.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpmanager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helptopic.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/rstparser.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/boxutilities.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/mshift.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc-simd.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/rmpbc.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/seed.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/forcetable.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 CubicSplineTable::CubicSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 QuadraticSplineTable::QuadraticSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 std::vector thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing)); ^ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/cyclecounter.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/wallcycle.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/walltime_accounting.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomprop.cpp /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'std::vector gmx::internal::vectorSecondDerivative(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 vectorSecondDerivative(ArrayRef f, double spacing) ^~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef, gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 throwUnlessDerivativeIsConsistentWithFunction(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atoms.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomsbuilder.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/block.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/exclusionblocks.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/forcefieldparameters.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/idef.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/ifunc.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H 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-O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/futil.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/gmxassert.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/gmxomp.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/gmxregex.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/init.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/inmemoryserializer.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/int64_to_int.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetree.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/logger.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/loggerbuilder.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/messagestringcollector.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/niceheader.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/path.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/pleasecite.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/programcontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/smalloc.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/strconvert.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/strdb.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/stringstream.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/stringutil.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/sysinfo.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/textreader.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/textwriter.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/txtdump.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/confio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/enxio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/espio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/filetypes.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/g96io.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmx_internal_xdr.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio-xdr.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.h:44, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector gmx_fio_get_output_file_positions()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/groio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/libxdrf.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/matio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/md5.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/mtxio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/oenv.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/pdbio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/readinp.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/timecontrol.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tpxio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trrio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trxio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/warninp.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/writeps.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xdrd.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xtcio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xvgr.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/output.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull_rotation.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/awh.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/bias.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void Bias::updateForceCorrelationGrid(gmx::ArrayRef probWeightNeighbor, ^~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:70: /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 updateForceCorrelationGrid(probWeightNeighbor, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tempForce_, biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.h:53, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biassharing.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biaswriter.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef, const gmx::BiasParams&)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void updateTargetDistribution(gmx::ArrayRef pointState, ^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector&, const gmx::Grid&, int, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::calcUmbrellaForceAndPotential(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::calcConvolvedForce(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::moveUmbrella(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleProbabilityWeights(const Grid &grid, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleCoordAndPmf(const Grid &grid, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 CoordState::sampleUmbrellaGridpoint(const Grid &grid, ^~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector*)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/grid.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef, bool, double)': /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void CorrelationTensor::addData(double weight, ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector&, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSize(const BiasParams ¶ms, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/pointstate.cpp /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/read-params.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/support.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector&, const gmx::AwhDimParams*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imd.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imdsocket.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/chargegroup.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/conformation-utilities.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/network.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/forcerec.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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/build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/lincs.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/md_support.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin_bar.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdsetup.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/membed.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_atomdata.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 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/build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nsgrid.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/perf_est.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gamess.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gaussian.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_mopac.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_orca.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qmmm.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/resethandler.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rf_util.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 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/build/gromacs-2019.1/src/gromacs/mdlib/shake.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/sighandler.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/long-range-correction.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gather.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-load-balancing.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-pp.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-solve.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program-impl.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/cpuinfo.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/detecthardware.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/gpu_hw_info.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/hardwaretopology.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/printhardware.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/identifyavx512fmaunits.cpp cd 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/logging.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp cd 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/multisim.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/replicaexchange.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp cd 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/handlerestart.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/mdmodules.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractoption.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractsection.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/behaviorcollection.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/options.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsassigner.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate::ValueList*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsection.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsvisitor.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/timeunitmanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/treesupport.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/manager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/bin/ranlib ../../lib/libgromacs_mdrun_mpi.mpich.a make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/programs /build/gromacs-2019.1/build/mpich/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/mdrun.dir/mdrun_main.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun_main.cpp cd /build/gromacs-2019.1/build/mpich/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun.dir/mdrun_main.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../bin/mdrun_mpi.mpich -Wl,-rpath,:::::::::::::::::::::::::::::::::: ../../lib/libgromacs_mdrun_mpi.mpich.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich/CMakeFiles 0 make[1]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -j3 -C build/mpich-dp make[1]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 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'/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build Scanning dependencies of target libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 1%] Built target libgromacs_external cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 3%] Built target tng_io_obj /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 5%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/programs /build/gromacs-2019.1/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 5%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/mpich-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/filenm.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/pargs.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/shellcompletions.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/viewit.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/atomdistribution.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/box.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/cellsizes.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp /build/gromacs-2019.1/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef >, const MPI_Comm*, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:235:13: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 static void low_set_ddbox(int numPbcDimensions, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef >, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void set_ddbox(const gmx_domdec_t &dd, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 low_set_ddbox(dd.npbcdim, dd.numBoundedDimensions, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &dd.nc, box, calculateUnboundedSize, xRef, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddbox); ~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef >, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:308:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void set_ddbox_cr(const t_commrec &cr, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:317:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dd_nc, box, true, x, nullptr, ddbox); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/distribute.cpp /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef >, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void dd_collect_vec(gmx_domdec_t *dd, ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)': /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:310:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->x), globalXRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:315:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->v), globalVRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:320:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->cg_p), globalCgpRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlb.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlbtiming.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_constraints.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(const gmx_domdec_t *dd, ^~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef, gmx::ArrayRef) [with T = gmx::BasicVector]': /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_setup.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const t_state&, real)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:3015:14: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, false, state.box, true, state.x, &ddbox); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_specatomcomm.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void set_dd_limits_and_grid(const gmx::MDLogger&, t_commrec*, gmx_domdec_t*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef >, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2137:13: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 static void set_dd_limits_and_grid(const gmx::MDLogger &mdlog, ^~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2358:21: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox_cr(*cr, &dd->nc, *ir, box, xGlobal, ddbox); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2383:21: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox_cr(*cr, nullptr, *ir, box, xGlobal, ddbox); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_topology.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'gmx_domdec_t* init_domain_decomposition(const gmx::MDLogger&, t_commrec*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef >, gmx::LocalAtomSetManager*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2953:15: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 gmx_domdec_t *init_domain_decomposition(const gmx::MDLogger &mdlog, ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2979:27: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_dd_limits_and_grid(mdlog, cr, dd, options, mdrunOptions, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mtop, ir, ~~~~~~~~~ box, xGlobal, ~~~~~~~~~~~~~ &ddbox); ~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_vsite.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(dd, d, dddirBackward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(dd, d, dddirForward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, real (*)[3], gmx::ArrayRef >, gmx_wallcycle*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:296:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void dd_move_x(gmx_domdec_t *dd, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 ddSendrecv(dd, d, dddirBackward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ArrayRef >, real (*)[3], gmx_wallcycle*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:408:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void dd_move_f(gmx_domdec_t *dd, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 ddSendrecv(dd, d, dddirForward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dump.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/ga2la.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomset.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetdata.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/redistribute.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/utility.cpp /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)': /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(dd, d, dddirBackward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ gmx::arrayRefFromArray(&buf_s[0].min0, numReals), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gmx::arrayRefFromArray(&buf_r[0].min0, numReals)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/utility.h:45, from /build/gromacs-2019.1/src/gromacs/domdec/utility.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/utility.h:45, from /build/gromacs-2019.1/src/gromacs/domdec/utility.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, gmx::PaddedVector >*, int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/3dtransforms.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/do_fit.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/functions.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/invertmatrix.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/units.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/utilities.cpp /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, gmx::PaddedVector >*)': /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 ddSendrecv(dd, dim_ind, dddirBackward, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ work.positionBuffer, rvecBufferRef); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/veccompare.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/vecdump.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/df_history.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/iforceprovider.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/inputrec.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/md_enums.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/observableshistory.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t*, const t_inputrec*, t_state*, gmx::PaddedVector >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)': /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3244:18: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, true, ~~~~~~~~~^~~~~~~~~~~ DDMASTER(dd) ? state_global->box : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ true, xGlobal, ~~~~~~~~~~~~~~ &ddbox); ~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3297:18: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, bMasterState, state_local->box, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ true, state_local->x, &ddbox); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3316:18: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, bMasterState, state_local->box, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bNStGlobalComm, state_local->x, &ddbox); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_local->x); ~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_local->x); ~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3419:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid(fr->nbv->nbs.get(), fr->ePBC, state_local->box, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, ~~ comm->zones.size[0].bb_x0, ~~~~~~~~~~~~~~~~~~~~~~~~~~ comm->zones.size[0].bb_x1, ~~~~~~~~~~~~~~~~~~~~~~~~~~ comm->updateGroupsCog.get(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, dd->ncg_home, ~~~~~~~~~~~~~~~~ comm->zones.dens_zone0, ~~~~~~~~~~~~~~~~~~~~~~~ fr->cginfo, ~~~~~~~~~~~ state_local->x, ~~~~~~~~~~~~~~~ ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->nbv->grp[eintLocal].kernel_type, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->nbv->nbat); ~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef >, gmx::index))[3]': /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:207:7: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 rvec *makeRvecArray(gmx::ArrayRef v, ^~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpformat.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpmanager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helptopic.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/rstparser.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/boxutilities.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/mshift.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc-simd.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/rmpbc.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/seed.cpp /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1413:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef x) ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1473:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tabulatednormaldistribution.cpp /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/forcetable.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 CubicSplineTable::CubicSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 QuadraticSplineTable::QuadraticSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 std::vector thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing)); ^ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/cyclecounter.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/wallcycle.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/walltime_accounting.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomprop.cpp /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'std::vector gmx::internal::vectorSecondDerivative(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 vectorSecondDerivative(ArrayRef f, double spacing) ^~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef, gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 throwUnlessDerivativeIsConsistentWithFunction(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atoms.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomsbuilder.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/block.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/exclusionblocks.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/forcefieldparameters.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/idef.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/ifunc.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/index.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/invblock.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/mtop_util.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/residuetypes.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/symtab.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/topology.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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/build/gromacs-2019.1/src/gromacs/utility/alignedallocator.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/basenetwork.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/baseversion.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/fatalerror.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c 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-isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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-I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/messagestringcollector.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/niceheader.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/programcontext.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/stringstream.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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/build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/txtdump.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/variant.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/variant.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/confio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/enxio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/espio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/filetypes.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/g96io.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmx_internal_xdr.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio-xdr.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.h:44, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector gmx_fio_get_output_file_positions()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/groio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/libxdrf.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/matio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/md5.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/mtxio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/oenv.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/pdbio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/readinp.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/timecontrol.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tpxio.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.h:42, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.h:42, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trrio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trxio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/warninp.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/writeps.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xdrd.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xtcio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xvgr.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp:51: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void init_swapcoords(FILE*, t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const MdrunOptions&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/output.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp:46: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::unique_ptr ed_open(int, ObservablesHistory*, const char*, const char*, gmx_bool, const gmx_output_env_t*, const t_commrec*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull_rotation.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/awh.cpp /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef >, const t_pbc&, int, real)': /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:950:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 bool pullCheckPbcWithinGroup(const pull_t &pull, ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/bias.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void Bias::updateForceCorrelationGrid(gmx::ArrayRef probWeightNeighbor, ^~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:70: /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 updateForceCorrelationGrid(probWeightNeighbor, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tempForce_, biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biassharing.cpp /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.h:53, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biaswriter.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef, const gmx::BiasParams&)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void updateTargetDistribution(gmx::ArrayRef pointState, ^~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector&, const gmx::Grid&, int, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::calcUmbrellaForceAndPotential(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::calcConvolvedForce(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::moveUmbrella(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleProbabilityWeights(const Grid &grid, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleCoordAndPmf(const Grid &grid, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 CoordState::sampleUmbrellaGridpoint(const Grid &grid, ^~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector*)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/grid.cpp /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef, bool, double)': /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void CorrelationTensor::addData(double weight, ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/pointstate.cpp /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector&, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSize(const BiasParams ¶ms, ^~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/read-params.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/support.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector&, const gmx::AwhDimParams*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imd.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imdsocket.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/chargegroup.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/conformation-utilities.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/network.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nrnb.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_generic.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic_cg.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_generic_cg.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nonbonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nonbonded.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/boxdeformation.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/calc_verletbuf.cpp /build/gromacs-2019.1/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef >, real (*)[3], int64_t)': /build/gromacs-2019.1/src/gromacs/mdlib/boxdeformation.cpp:109:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 BoxDeformation::apply(ArrayRef x, ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/calcmu.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/mdlib/calc_verletbuf.h:39, from /build/gromacs-2019.1/src/gromacs/mdlib/calc_verletbuf.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector get_verlet_buffer_atomtypes(const gmx_mtop_t*, bool, int*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef >, const real*, const real*, int, double*, double*)': /build/gromacs-2019.1/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void calc_mu(int start, int homenr, gmx::ArrayRef x, const real q[], const real qB[], ^~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/calcvir.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/checkpointhandler.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/compute_io.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.h:48, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/constr.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.h:48, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/constraintrange.cpp /build/gromacs-2019.1/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef, gmx_bool, int, int, int, int*, real, real, real*, int*)': /build/gromacs-2019.1/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 static void constr_recur(const t_blocka *at2con, ^~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/coupling.cpp /build/gromacs-2019.1/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef, gmx::FlexibleConstraintTreatment)': /build/gromacs-2019.1/src/gromacs/mdlib/constr.cpp:848:10: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 t_blocka make_at2con(const gmx_moltype_t &moltype, ^~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ebin.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/expanded.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/force.cpp /build/gromacs-2019.1/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef >, real, const gmx_bool*, const real*)': /build/gromacs-2019.1/src/gromacs/mdlib/coupling.cpp:781:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void andersen_tcoupl(const t_inputrec *ir, int64_t step, ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/force.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef, t_lambda*)': /build/gromacs-2019.1/src/gromacs/mdlib/force.cpp:698:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void sum_dhdl(gmx_enerdata_t *enerd, gmx::ArrayRef lambda, t_lambda *fepvals) ^~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/forcerec.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/groupcoord.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/lincs.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/md_support.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function 'void atoms2md(const gmx_mtop_t*, const t_inputrec*, int, const int*, int, gmx::MDAtoms*)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin_bar.cpp /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, gmx_mtop_t*, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void mdoutf_write_to_trajectory_files(FILE *fplog, const t_commrec *cr, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:269:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->x), globalXRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:274:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->v), globalVRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:280:27: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state_local, f_local, gmx::arrayRefFromArray(reinterpret_cast(f_global), f_local.size())); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdsetup.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/membed.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_atomdata.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid(nbnxn_search_t, int, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, int, int, real, const int*, gmx::ArrayRef >, int, const int*, int, nbnxn_atomdata_t*)': /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp:1416:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void nbnxn_put_on_grid(nbnxn_search_t nbs, ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nbnxn_search_t, const gmx_domdec_zones_t*, const int*, gmx::ArrayRef >, int, nbnxn_atomdata_t*)': /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp:1520:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs, ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp:1536:26: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid(nbs, nbs->ePBC, nullptr, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ zone, c0, c1, ~~~~~~~~~~~~~ nullptr, ~~~~~~~~ zones->cg_range[zone], ~~~~~~~~~~~~~~~~~~~~~~ zones->cg_range[zone+1], ~~~~~~~~~~~~~~~~~~~~~~~~ -1, ~~~ atinfo, ~~~~~~~ x, ~~ 0, nullptr, ~~~~~~~~~~~ nb_kernel_type, ~~~~~~~~~~~~~~~ nbat); ~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nsgrid.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/perf_est.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gamess.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gaussian.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_mopac.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_orca.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qmmm.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 int add_binr(t_bin *b, gmx::ArrayRef r) ^~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void extract_binr(t_bin *b, int index, gmx::ArrayRef r) ^~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/resethandler.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rf_util.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/settle.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/shake.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/sighandler.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/simulationsignal.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/splitter.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx_bool, int, gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, t_state*, gmx::ArrayRefWithPadding >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, const gmx_groups_t*, gmx_shellfc_t*, t_forcerec*, gmx::PpForceWorkload*, double, real*, const gmx_vsite_t*, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:1144:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdstep, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forceWithPadding[Min], force_vir, md, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:1254:17: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1, nrnb, wcycle, ~~~~~~~~~~~~~~~~ top, groups, state->box, posWithPadding[Try], &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forceWithPadding[Try], force_vir, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ md, enerd, fcd, state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shellfc_flags, ~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void computeSpecialForces(FILE*, const t_commrec*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, double, gmx_wallcycle_t, ForceProviders*, real (*)[3], gmx::ArrayRef >, const t_mdatoms*, real*, int, gmx::ForceWithVirial*, gmx_enerdata_t*, gmx_edsam*, gmx_bool)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:796:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 computeSpecialForces(FILE *fplog, ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, t_nrnb*, gmx_wallcycle_t, gmx_localtop_t*, const gmx_groups_t*, real (*)[3], gmx::ArrayRefWithPadding >, history_t*, gmx::ArrayRefWithPadding >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef, t_graph*, t_forcerec*, gmx::PpForceWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2119:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void do_force(FILE *fplog, ^~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1175:30: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid(nbv->nbs.get(), fr->ePBC, box, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, vzero, box_diag, ~~~~~~~~~~~~~~~~~~~ nullptr, 0, mdatoms->homenr, -1, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->cginfo, x.unpaddedArrayRef(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, nullptr, ~~~~~~~~~~~ nbv->grp[eintLocal].kernel_type, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nbv->nbat); ~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid_nonlocal(nbv->nbs.get(), domdec_zones(cr->dd), ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->cginfo, x.unpaddedArrayRef(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nbv->grp[eintNonlocal].kernel_type, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nbv->nbat); ~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1575:25: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation, ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, t, wcycle, ~~~~~~~~~~~~~~~~ fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ flags, &forceWithVirial, enerd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ed, bNS); ~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1626:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2047:25: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation, ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, t, wcycle, ~~~~~~~~~~~~~~~~ fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ flags, &forceWithVirial, enerd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ed, bNS); ~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2058:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2069:26: note: parameter passing for argument of type 'const gmx::ArrayRef >' changed in GCC 7.1 dd_move_f(cr->dd, forceWithVirial.force_, nullptr, wcycle); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/stat.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/stophandler.cpp /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2721:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef x) ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void initialize_lambdas(FILE*, t_inputrec*, int*, gmx::ArrayRef, double*)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2874:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef lambda, double *lam0) ^~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void init_md(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, double*, double*, t_state*, double*, t_nrnb*, gmx_mtop_t*, gmx_update_t**, gmx::BoxDeformation*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, real (*)[3], real (*)[3], real (*)[3], real (*)[3], real*, gmx_bool*, t_vcm**, gmx_wallcycle_t)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void init_rerun(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, t_state*, double*, t_nrnb*, gmx_mtop_t*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tgroup.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/updategroups.cpp /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, t_mdebin*, gmx_ekindata_t*, gmx::ArrayRef >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)': /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp:57:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(FILE *fplog, ^~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp:164:41: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, t, state, state_global, observablesHistory, f); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], t_state*, t_nrnb*, gmx_update_t*)': /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:1781:27: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 upd->deform->apply(localX, state->box, step); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef >, const gmx_update_t*, const gmx::Constraints*)': /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:1920:17: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 extern gmx_bool update_randomize_velocities(const t_inputrec *ir, int64_t step, const t_commrec *cr, ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:1944:24: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 andersen_tcoupl(ir, step, cr, md, v, rate, ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ upd->sd->randomize_group, upd->sd->boltzfac); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector&}; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/update.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp:85:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void UpdateGroupsCog::addCogs(gmx::ArrayRef globalAtomIndices, ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp:45: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/update.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function 'void update_realloc(gmx_update_t*, int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'gmx_update_t* init_update(const t_inputrec*, gmx::BoxDeformation*)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/vcm.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/wall.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/wnblist.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/bonded.cpp /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp:758:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void constructVsitesGlobal(const gmx_mtop_t &mtop, ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.h:44, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.h:44, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.3': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/disre.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/gpubonded-impl.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/listed-forces.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-internal.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/listed-internal.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/manage-threading.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/manage-threading.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/orires.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/orires.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/pairs.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/pairs.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/position-restraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/position-restraints.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/restcbt.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/restcbt.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/calculate-spline-moduli.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/ewald.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald-utils.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/ewald-utils.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/long-range-correction.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gather.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-grid.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-load-balancing.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-pp.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-redistribute.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-solve.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = gmx::BasicVector]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spline-work.cpp /usr/include/c++/8/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spread.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program-impl.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/calcgrid.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft5d.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/parallel_3dfft.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft_fftw3.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/cpuinfo.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/detecthardware.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/gpu_hw_info.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/hardwaretopology.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/printhardware.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/integrator.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/integrator.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/logging.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/multisim.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/replicaexchange.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &state->s, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->f); ~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:564:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, &state->s, makeArrayRef(state->s.x), globalXRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:869:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, nullptr, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ count, nrnb, wcycle, top, &top_global->groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ems->s.lambda, graph, fr, ppForceWorkload, vsite, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bNS ? GMX_FORCE_NS : 0), ~~~~~~~~~~~~~~~~~~~~~~~~~ DOMAINDECOMP(cr) ? ~~~~~~~~~~~~~~~~~~ DdOpenBalanceRegionBeforeForceComputation::yes : ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdOpenBalanceRegionBeforeForceComputation::no, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DOMAINDECOMP(cr) ? ~~~~~~~~~~~~~~~~~~ DdCloseBalanceRegionAfterForceComputation::yes : ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdCloseBalanceRegionAfterForceComputation::no); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:936:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_md()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:875:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bNS ? GMX_FORCE_NS : 0) | force_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1026:25: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1051:33: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ir, state, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, fr, ~~~~~~~~~~~~~~~ outf, mdebin, ekind, f, ~~~~~~~~~~~~~~~~~~~~~~~ checkpointHandler->isCheckpointingStep(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bRerunMD, bLastStep, ~~~~~~~~~~~~~~~~~~~~ mdrunOptions.writeConfout, ~~~~~~~~~~~~~~~~~~~~~~~~~~ bSumEkinhOld); ~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1089:55: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, upd, constr); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1292:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, const gmx_multisim_t*, gmx::IMDOutputProvider*, t_inputrec*, const MdrunOptions&, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t**, t_nrnb*, real*, t_forcerec*, gmx_enerdata_t**, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, nullptr); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_lbfgs()': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:1932:41: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), &ems.s, state_global, observablesHistory, ems.f); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_rerun()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:582:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, ir, awh, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, ed, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_NS | force_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:599:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ir, state, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, fr, ~~~~~~~~~~~~~~~ outf, mdebin, ekind, f, ~~~~~~~~~~~~~~~~~~~~~~~ isCheckpointingStep, doRerun, isLastStep, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdrunOptions.writeConfout, ~~~~~~~~~~~~~~~~~~~~~~~~~~ bSumEkinhOld); ~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:663:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:53: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, const gmx::PaddedVector >*, em_state_t*, gmx::Constraints*, int64_t)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_cg()': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &state->s, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->f); ~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:53: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_mimic()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:465:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, ir, awh, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, ed, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_NS | force_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:482:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ir, state, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, fr, ~~~~~~~~~~~~~~~ outf, mdebin, ekind, f, ~~~~~~~~~~~~~~~~~~~~~~~ isCheckpointingStep, doRerun, isLastStep, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdrunOptions.writeConfout, ~~~~~~~~~~~~~~~~~~~~~~~~~~ bSumEkinhOld); ~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:53: /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:544:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state, flocal, ftemp); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:554:45: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mimicCommunicator.sendForces(ftemp, state_global->natoms); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:569:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_steep()': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &state->s, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->f); ~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/handlerestart.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/mdmodules.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.h:50, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:46: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp:55: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.h:50, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:46: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = gmx::BasicVector]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp: In member function 'int gmx::Mdrunner::mdrunner()': /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:913:43: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cr->dd = init_domain_decomposition(mdlog, cr, domdecOptions, mdrunOptions, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &mtop, inputrec, ~~~~~~~~~~~~~~~~ box, positionsFromStatePointer(globalState.get()), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &atomSets); ~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:1269:38: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 constructVsitesGlobal(mtop, globalState->x); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp:55: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_tpi()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp:647:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, nullptr, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, &top_global->groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_global->box, state_global->x.arrayRefWithPadding(), &state_global->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_global->lambda, ~~~~~~~~~~~~~~~~~~~~~ nullptr, fr, ppForceWorkload, nullptr, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS : 0) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bStateChanged ? GMX_FORCE_STATECHANGED : 0), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdOpenBalanceRegionBeforeForceComputation::no, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdCloseBalanceRegionAfterForceComputation::no); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractoption.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractsection.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/behaviorcollection.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/options.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsassigner.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsection.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate::ValueList*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsvisitor.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/timeunitmanager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/treesupport.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/manager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:60, from /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.h:49, from /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.cpp:38: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr, const std::vector&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /build/gromacs-2019.1/src/gromacs/mimic/MimicUtils.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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'/build/gromacs-2019.1/build/mpich-dp' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/programs /build/gromacs-2019.1/build/mpich-dp/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src 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../../lib/libgromacs_mdrun_mpi_d.mpich.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich-dp/CMakeFiles 0 make[1]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' sed -e 's/#MPIABBR#/mpich/g' -e 's/#MPIPROG#/MPICH/g' \ < debian/gromacs-parallel.README.Debian.in \ > debian/gromacs-mpich.README.Debian touch build-mpich dh_testdir /usr/bin/make -j3 -C build/openmpi make[1]: Entering directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/cmake -S/build/gromacs-2019.1 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libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/system_error.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 1%] Built target libgromacs_external cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 2%] Built target lmfit_objlib cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/programs /build/gromacs-2019.1/build/openmpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 2%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 5%] Built target tng_io_obj cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 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/build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/openmpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/filenm.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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-isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/distribute.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlb.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlbtiming.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && 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-isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_constraints.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_topology.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 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-I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomset.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetdata.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/redistribute.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/utility.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/3dtransforms.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/do_fit.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/functions.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/invertmatrix.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/units.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/utilities.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/veccompare.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/vecdump.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/df_history.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/iforceprovider.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/inputrec.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/md_enums.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/observableshistory.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpformat.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpmanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helptopic.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/rstparser.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/boxutilities.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/mshift.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc-simd.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/rmpbc.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/seed.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/forcetable.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 CubicSplineTable::CubicSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 QuadraticSplineTable::QuadraticSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 std::vector thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing)); ^ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/cyclecounter.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/wallcycle.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/walltime_accounting.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomprop.cpp /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'std::vector gmx::internal::vectorSecondDerivative(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 vectorSecondDerivative(ArrayRef f, double spacing) ^~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef, gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 throwUnlessDerivativeIsConsistentWithFunction(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atoms.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomsbuilder.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/block.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/exclusionblocks.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/forcefieldparameters.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG 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-DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/index.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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/usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/symtab.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/topology.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/topsort.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/alignedallocator.cpp cd 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-isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/baseversion.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/binaryinformation.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/compare.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/coolstuff.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src 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/build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/datafilefinder.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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-DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/errorformat.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/exceptions.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/fatalerror.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/fileredirector.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/filestream.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/futil.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/gmxassert.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/gmxomp.cpp cd 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/init.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/inmemoryserializer.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/int64_to_int.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetree.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/logger.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/messagestringcollector.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/niceheader.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/path.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/pleasecite.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/programcontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/smalloc.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/strconvert.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/strdb.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/stringstream.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/stringutil.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/sysinfo.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/textreader.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/textwriter.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/txtdump.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/variant.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/variant.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/confio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/enxio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/espio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/filetypes.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/g96io.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmx_internal_xdr.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio-xdr.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.h:44, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector gmx_fio_get_output_file_positions()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/groio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/libxdrf.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/matio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/md5.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/mtxio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/oenv.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/pdbio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/readinp.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/timecontrol.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tpxio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trrio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trxio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/warninp.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/writeps.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xdrd.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xtcio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xvgr.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/output.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull_rotation.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/awh.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/bias.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void Bias::updateForceCorrelationGrid(gmx::ArrayRef probWeightNeighbor, ^~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:70: /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 updateForceCorrelationGrid(probWeightNeighbor, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tempForce_, biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biassharing.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.h:53, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biaswriter.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef, const gmx::BiasParams&)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void updateTargetDistribution(gmx::ArrayRef pointState, ^~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector&, const gmx::Grid&, int, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::calcUmbrellaForceAndPotential(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::calcConvolvedForce(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::moveUmbrella(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleProbabilityWeights(const Grid &grid, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleCoordAndPmf(const Grid &grid, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 CoordState::sampleUmbrellaGridpoint(const Grid &grid, ^~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector*)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/grid.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef, bool, double)': /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void CorrelationTensor::addData(double weight, ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector&, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSize(const BiasParams ¶ms, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/pointstate.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/read-params.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/support.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector&, const gmx::AwhDimParams*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imd.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imdsocket.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/chargegroup.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/conformation-utilities.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/network.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/md_support.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin_bar.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdsetup.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/membed.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_atomdata.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o 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/build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/simulationsignal.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-grid.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-redistribute.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-solve.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spline-work.cpp cd 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft5d.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 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CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft_fftw3.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/hardwaretopology.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/logging.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/multisim.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/mdmodules.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/behaviorcollection.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/options.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsassigner.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsection.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate::ValueList*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsvisitor.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/timeunitmanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/treesupport.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/manager.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/taskassignment.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectory/energyframe.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectory/trajectoryframe.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG 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-I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops 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src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi 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-ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/system_error.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 1%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 2%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/programs /build/gromacs-2019.1/build/openmpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 2%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 5%] Built target tng_io_obj cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/openmpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/filenm.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/pargs.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/shellcompletions.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/viewit.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/atomdistribution.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/box.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/cellsizes.cpp /build/gromacs-2019.1/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef >, ompi_communicator_t* const*, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:235:13: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 static void low_set_ddbox(int numPbcDimensions, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef >, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void set_ddbox(const gmx_domdec_t &dd, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 low_set_ddbox(dd.npbcdim, dd.numBoundedDimensions, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &dd.nc, box, calculateUnboundedSize, xRef, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddbox); ~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef >, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:308:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void set_ddbox_cr(const t_commrec &cr, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/box.cpp:317:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dd_nc, box, true, x, nullptr, ddbox); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/distribute.cpp /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef >, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void dd_collect_vec(gmx_domdec_t *dd, ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)': /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:310:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->x), globalXRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:315:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->v), globalVRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:320:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->cg_p), globalCgpRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlb.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlbtiming.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_constraints.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(const gmx_domdec_t *dd, ^~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef, gmx::ArrayRef) [with T = gmx::BasicVector]': /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_setup.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const t_state&, real)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:3015:14: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, false, state.box, true, state.x, &ddbox); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_specatomcomm.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void set_dd_limits_and_grid(const gmx::MDLogger&, t_commrec*, gmx_domdec_t*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef >, gmx_ddbox_t*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2137:13: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 static void set_dd_limits_and_grid(const gmx::MDLogger &mdlog, ^~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2358:21: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox_cr(*cr, &dd->nc, *ir, box, xGlobal, ddbox); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2383:21: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox_cr(*cr, nullptr, *ir, box, xGlobal, ddbox); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_topology.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'gmx_domdec_t* init_domain_decomposition(const gmx::MDLogger&, t_commrec*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef >, gmx::LocalAtomSetManager*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2953:15: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 gmx_domdec_t *init_domain_decomposition(const gmx::MDLogger &mdlog, ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:2979:27: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_dd_limits_and_grid(mdlog, cr, dd, options, mdrunOptions, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mtop, ir, ~~~~~~~~~ box, xGlobal, ~~~~~~~~~~~~~ &ddbox); ~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(dd, d, dddirBackward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(dd, d, dddirForward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_vsite.cpp /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, real (*)[3], gmx::ArrayRef >, gmx_wallcycle*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:296:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void dd_move_x(gmx_domdec_t *dd, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 ddSendrecv(dd, d, dddirBackward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ArrayRef >, real (*)[3], gmx_wallcycle*)': /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:408:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void dd_move_f(gmx_domdec_t *dd, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 ddSendrecv(dd, d, dddirForward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ sendBuffer, receiveBuffer); ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dump.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/ga2la.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomset.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetdata.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/redistribute.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/utility.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/utility.h:45, from /build/gromacs-2019.1/src/gromacs/domdec/utility.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)': /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 ddSendrecv(dd, d, dddirBackward, ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ gmx::arrayRefFromArray(&buf_s[0].min0, numReals), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gmx::arrayRefFromArray(&buf_r[0].min0, numReals)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/utility.h:45, from /build/gromacs-2019.1/src/gromacs/domdec/utility.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, gmx::PaddedVector >*, int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/3dtransforms.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/do_fit.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/functions.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/invertmatrix.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/units.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/utilities.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/veccompare.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/vecdump.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/df_history.cpp /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, gmx::PaddedVector >*)': /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 ddSendrecv(dd, dim_ind, dddirBackward, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ work.positionBuffer, rvecBufferRef); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/iforceprovider.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/inputrec.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/md_enums.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/observableshistory.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t*, const t_inputrec*, t_state*, gmx::PaddedVector >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)': /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3244:18: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, true, ~~~~~~~~~^~~~~~~~~~~ DDMASTER(dd) ? state_global->box : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ true, xGlobal, ~~~~~~~~~~~~~~ &ddbox); ~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3297:18: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, bMasterState, state_local->box, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ true, state_local->x, &ddbox); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3316:18: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 set_ddbox(*dd, bMasterState, state_local->box, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bNStGlobalComm, state_local->x, &ddbox); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_local->x); ~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_local->x); ~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp:3419:34: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid(fr->nbv->nbs.get(), fr->ePBC, state_local->box, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, ~~ comm->zones.size[0].bb_x0, ~~~~~~~~~~~~~~~~~~~~~~~~~~ comm->zones.size[0].bb_x1, ~~~~~~~~~~~~~~~~~~~~~~~~~~ comm->updateGroupsCog.get(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, dd->ncg_home, ~~~~~~~~~~~~~~~~ comm->zones.dens_zone0, ~~~~~~~~~~~~~~~~~~~~~~~ fr->cginfo, ~~~~~~~~~~~ state_local->x, ~~~~~~~~~~~~~~~ ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->nbv->grp[eintLocal].kernel_type, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->nbv->nbat); ~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef >, gmx::index))[3]': /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:207:7: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 rvec *makeRvecArray(gmx::ArrayRef v, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpformat.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpmanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helptopic.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/rstparser.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/boxutilities.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/mshift.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc-simd.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/rmpbc.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/seed.cpp /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1413:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef x) ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1473:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/forcetable.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 CubicSplineTable::CubicSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 QuadraticSplineTable::QuadraticSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 std::vector thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing)); ^ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/cyclecounter.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/wallcycle.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/walltime_accounting.cpp /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomprop.cpp /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'std::vector gmx::internal::vectorSecondDerivative(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 vectorSecondDerivative(ArrayRef f, double spacing) ^~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef, gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 throwUnlessDerivativeIsConsistentWithFunction(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atoms.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomsbuilder.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/block.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/exclusionblocks.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/fatalerror.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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-I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/gmxassert.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/gmxomp.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/init.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/inmemoryserializer.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/int64_to_int.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetree.cpp cd 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/logger.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/path.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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-I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/smalloc.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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-fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/strdb.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/stringstream.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/stringutil.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/sysinfo.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/textreader.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/textwriter.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/txtdump.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/variant.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/variant.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/confio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/enxio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/espio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/filetypes.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/g96io.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmx_internal_xdr.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio-xdr.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.h:44, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector gmx_fio_get_output_file_positions()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/groio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/libxdrf.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/matio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/md5.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/mtxio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/oenv.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/pdbio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/readinp.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/timecontrol.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tpxio.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.h:42, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.h:42, from /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trrio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trxio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/warninp.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/writeps.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xdrd.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xtcio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xvgr.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp:51: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void init_swapcoords(FILE*, t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const MdrunOptions&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/output.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp:46: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::unique_ptr ed_open(int, ObservablesHistory*, const char*, const char*, gmx_bool, const gmx_output_env_t*, const t_commrec*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull_rotation.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/awh.cpp /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef >, const t_pbc&, int, real)': /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:950:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 bool pullCheckPbcWithinGroup(const pull_t &pull, ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/bias.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void Bias::updateForceCorrelationGrid(gmx::ArrayRef probWeightNeighbor, ^~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:70: /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 updateForceCorrelationGrid(probWeightNeighbor, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tempForce_, biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biassharing.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.h:53, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biaswriter.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef, const gmx::BiasParams&)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void updateTargetDistribution(gmx::ArrayRef pointState, ^~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector&, const gmx::Grid&, int, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::calcUmbrellaForceAndPotential(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::calcConvolvedForce(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::moveUmbrella(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleProbabilityWeights(const Grid &grid, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleCoordAndPmf(const Grid &grid, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 CoordState::sampleUmbrellaGridpoint(const Grid &grid, ^~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector*)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/grid.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef, bool, double)': /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void CorrelationTensor::addData(double weight, ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector&, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSize(const BiasParams ¶ms, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/pointstate.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/read-params.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/support.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector&, const gmx::AwhDimParams*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imd.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imdsocket.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/chargegroup.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/conformation-utilities.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/network.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nrnb.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_generic.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic_cg.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_generic_cg.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nonbonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nonbonded.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/boxdeformation.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/calc_verletbuf.cpp /build/gromacs-2019.1/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef >, real (*)[3], int64_t)': /build/gromacs-2019.1/src/gromacs/mdlib/boxdeformation.cpp:109:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 BoxDeformation::apply(ArrayRef x, ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/calcmu.cpp /build/gromacs-2019.1/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef >, const real*, const real*, int, double*, double*)': /build/gromacs-2019.1/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void calc_mu(int start, int homenr, gmx::ArrayRef x, const real q[], const real qB[], ^~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/calcvir.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/mdlib/calc_verletbuf.h:39, from /build/gromacs-2019.1/src/gromacs/mdlib/calc_verletbuf.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'std::vector get_verlet_buffer_atomtypes(const gmx_mtop_t*, bool, int*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.h:48, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/checkpointhandler.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.h:48, from /build/gromacs-2019.1/src/gromacs/mdlib/broadcaststructs.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/compute_io.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/constr.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/constraintrange.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/coupling.cpp /build/gromacs-2019.1/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef, gmx_bool, int, int, int, int*, real, real, real*, int*)': /build/gromacs-2019.1/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 static void constr_recur(const t_blocka *at2con, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef, gmx::FlexibleConstraintTreatment)': /build/gromacs-2019.1/src/gromacs/mdlib/constr.cpp:848:10: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 t_blocka make_at2con(const gmx_moltype_t &moltype, ^~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ebin.cpp /build/gromacs-2019.1/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef >, real, const gmx_bool*, const real*)': /build/gromacs-2019.1/src/gromacs/mdlib/coupling.cpp:781:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void andersen_tcoupl(const t_inputrec *ir, int64_t step, ^~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/expanded.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/force.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/forcerec.cpp /build/gromacs-2019.1/src/gromacs/mdlib/force.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef, t_lambda*)': /build/gromacs-2019.1/src/gromacs/mdlib/force.cpp:698:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void sum_dhdl(gmx_enerdata_t *enerd, gmx::ArrayRef lambda, t_lambda *fepvals) ^~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/groupcoord.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/lincs.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/md_support.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin_bar.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function 'void atoms2md(const gmx_mtop_t*, const t_inputrec*, int, const int*, int, gmx::MDAtoms*)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdsetup.cpp /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, gmx_mtop_t*, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void mdoutf_write_to_trajectory_files(FILE *fplog, const t_commrec *cr, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:269:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->x), globalXRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:274:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->v), globalVRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp:280:27: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state_local, f_local, gmx::arrayRefFromArray(reinterpret_cast(f_global), f_local.size())); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/membed.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_atomdata.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid(nbnxn_search_t, int, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, int, int, real, const int*, gmx::ArrayRef >, int, const int*, int, nbnxn_atomdata_t*)': /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp:1416:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void nbnxn_put_on_grid(nbnxn_search_t nbs, ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nbnxn_search_t, const gmx_domdec_zones_t*, const int*, gmx::ArrayRef >, int, nbnxn_atomdata_t*)': /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp:1520:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs, ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp:1536:26: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid(nbs, nbs->ePBC, nullptr, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ zone, c0, c1, ~~~~~~~~~~~~~ nullptr, ~~~~~~~~ zones->cg_range[zone], ~~~~~~~~~~~~~~~~~~~~~~ zones->cg_range[zone+1], ~~~~~~~~~~~~~~~~~~~~~~~~ -1, ~~~ atinfo, ~~~~~~~ x, ~~ 0, nullptr, ~~~~~~~~~~~ nb_kernel_type, ~~~~~~~~~~~~~~~ nbat); ~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nsgrid.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/perf_est.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gamess.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gaussian.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_mopac.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_orca.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qmmm.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/resethandler.cpp /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 int add_binr(t_bin *b, gmx::ArrayRef r) ^~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void extract_binr(t_bin *b, int index, gmx::ArrayRef r) ^~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rf_util.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/settle.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/shake.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/sighandler.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/simulationsignal.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/splitter.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx_bool, int, gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, t_state*, gmx::ArrayRefWithPadding >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, const gmx_groups_t*, gmx_shellfc_t*, t_forcerec*, gmx::PpForceWorkload*, double, real*, const gmx_vsite_t*, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:1144:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdstep, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forceWithPadding[Min], force_vir, md, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp:1254:17: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1, nrnb, wcycle, ~~~~~~~~~~~~~~~~ top, groups, state->box, posWithPadding[Try], &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forceWithPadding[Try], force_vir, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ md, enerd, fcd, state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shellfc_flags, ~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void computeSpecialForces(FILE*, const t_commrec*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, double, gmx_wallcycle_t, ForceProviders*, real (*)[3], gmx::ArrayRef >, const t_mdatoms*, real*, int, gmx::ForceWithVirial*, gmx_enerdata_t*, gmx_edsam*, gmx_bool)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:796:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 computeSpecialForces(FILE *fplog, ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, t_nrnb*, gmx_wallcycle_t, gmx_localtop_t*, const gmx_groups_t*, real (*)[3], gmx::ArrayRefWithPadding >, history_t*, gmx::ArrayRefWithPadding >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef, t_graph*, t_forcerec*, gmx::PpForceWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2119:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void do_force(FILE *fplog, ^~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1175:30: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid(nbv->nbs.get(), fr->ePBC, box, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, vzero, box_diag, ~~~~~~~~~~~~~~~~~~~ nullptr, 0, mdatoms->homenr, -1, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->cginfo, x.unpaddedArrayRef(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0, nullptr, ~~~~~~~~~~~ nbv->grp[eintLocal].kernel_type, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nbv->nbat); ~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 nbnxn_put_on_grid_nonlocal(nbv->nbs.get(), domdec_zones(cr->dd), ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fr->cginfo, x.unpaddedArrayRef(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nbv->grp[eintNonlocal].kernel_type, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nbv->nbat); ~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1575:25: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation, ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, t, wcycle, ~~~~~~~~~~~~~~~~ fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ flags, &forceWithVirial, enerd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ed, bNS); ~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:1626:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2047:25: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation, ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, t, wcycle, ~~~~~~~~~~~~~~~~ fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ flags, &forceWithVirial, enerd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ed, bNS); ~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2058:22: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2069:26: note: parameter passing for argument of type 'const gmx::ArrayRef >' changed in GCC 7.1 dd_move_f(cr->dd, forceWithVirial.force_, nullptr, wcycle); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/stat.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/stophandler.cpp /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2721:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef x) ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void initialize_lambdas(FILE*, t_inputrec*, int*, gmx::ArrayRef, double*)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2874:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef lambda, double *lam0) ^~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void init_md(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, double*, double*, t_state*, double*, t_nrnb*, gmx_mtop_t*, gmx_update_t**, gmx::BoxDeformation*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, real (*)[3], real (*)[3], real (*)[3], real (*)[3], real*, gmx_bool*, t_vcm**, gmx_wallcycle_t)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp: In function 'void init_rerun(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, t_state*, double*, t_nrnb*, gmx_mtop_t*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)': /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tgroup.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, t_mdebin*, gmx_ekindata_t*, gmx::ArrayRef >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)': /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp:57:1: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(FILE *fplog, ^~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp:164:41: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, t, state, state_global, observablesHistory, f); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/updategroups.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], t_state*, t_nrnb*, gmx_update_t*)': /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:1781:27: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 upd->deform->apply(localX, state->box, step); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector&}; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef >, const gmx_update_t*, const gmx::Constraints*)': /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:1920:17: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 extern gmx_bool update_randomize_velocities(const t_inputrec *ir, int64_t step, const t_commrec *cr, ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:1944:24: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 andersen_tcoupl(ir, step, cr, md, v, rate, ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ upd->sd->randomize_group, upd->sd->boltzfac); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp:85:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void UpdateGroupsCog::addCogs(gmx::ArrayRef globalAtomIndices, ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp:45: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/update.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/update.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function 'void update_realloc(gmx_update_t*, int)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'gmx_update_t* init_update(const t_inputrec*, gmx::BoxDeformation*)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/vcm.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/wall.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/wnblist.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/bonded.cpp /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef >)': /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp:758:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void constructVsitesGlobal(const gmx_mtop_t &mtop, ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.h:44, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/disre.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.h:44, from /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.3': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/gpubonded-impl.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/listed-forces.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-internal.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/listed-internal.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/manage-threading.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/manage-threading.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/orires.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/orires.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/pairs.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/pairs.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/position-restraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/position-restraints.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/restcbt.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/restcbt.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/calculate-spline-moduli.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/ewald.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald-utils.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/ewald-utils.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/long-range-correction.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gather.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-grid.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-load-balancing.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-pp.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-redistribute.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-solve.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spline-work.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp:72: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = gmx::BasicVector]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spread.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program-impl.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/calcgrid.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft5d.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/parallel_3dfft.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft_fftw3.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/cpuinfo.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/detecthardware.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/gpu_hw_info.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/hardwaretopology.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/printhardware.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/integrator.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/integrator.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/logging.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/multisim.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/replicaexchange.cpp /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &state->s, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->f); ~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:564:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, &state->s, makeArrayRef(state->s.x), globalXRef); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:869:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, nullptr, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ count, nrnb, wcycle, top, &top_global->groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ems->s.lambda, graph, fr, ppForceWorkload, vsite, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bNS ? GMX_FORCE_NS : 0), ~~~~~~~~~~~~~~~~~~~~~~~~~ DOMAINDECOMP(cr) ? ~~~~~~~~~~~~~~~~~~ DdOpenBalanceRegionBeforeForceComputation::yes : ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdOpenBalanceRegionBeforeForceComputation::no, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DOMAINDECOMP(cr) ? ~~~~~~~~~~~~~~~~~~ DdCloseBalanceRegionAfterForceComputation::yes : ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdCloseBalanceRegionAfterForceComputation::no); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:936:13: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_md()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:875:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bNS ? GMX_FORCE_NS : 0) | force_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1026:25: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1051:33: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ir, state, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, fr, ~~~~~~~~~~~~~~~ outf, mdebin, ekind, f, ~~~~~~~~~~~~~~~~~~~~~~~ checkpointHandler->isCheckpointingStep(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bRerunMD, bLastStep, ~~~~~~~~~~~~~~~~~~~~ mdrunOptions.writeConfout, ~~~~~~~~~~~~~~~~~~~~~~~~~~ bSumEkinhOld); ~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1089:55: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, upd, constr); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp:1292:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, const gmx_multisim_t*, gmx::IMDOutputProvider*, t_inputrec*, const MdrunOptions&, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t**, t_nrnb*, real*, t_forcerec*, gmx_enerdata_t**, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, nullptr); ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_lbfgs()': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:1932:41: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), &ems.s, state_global, observablesHistory, ems.f); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:53: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_rerun()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:582:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, ir, awh, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, ed, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_NS | force_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:599:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ir, state, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, fr, ~~~~~~~~~~~~~~~ outf, mdebin, ekind, f, ~~~~~~~~~~~~~~~~~~~~~~~ isCheckpointingStep, doRerun, isLastStep, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdrunOptions.writeConfout, ~~~~~~~~~~~~~~~~~~~~~~~~~~ bSumEkinhOld); ~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp:663:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, const gmx::PaddedVector >*, em_state_t*, gmx::Constraints*, int64_t)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:53: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_mimic()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:465:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, ir, awh, enforcedRotation, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->box, state->x.arrayRefWithPadding(), &state->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->lambda, graph, ~~~~~~~~~~~~~~~~~~~~~ fr, ppForceWorkload, vsite, mu_tot, t, ed, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_NS | force_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ddOpenBalanceRegion, ddCloseBalanceRegion); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:482:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ir, state, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, fr, ~~~~~~~~~~~~~~~ outf, mdebin, ekind, f, ~~~~~~~~~~~~~~~~~~~~~~~ isCheckpointingStep, doRerun, isLastStep, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdrunOptions.writeConfout, ~~~~~~~~~~~~~~~~~~~~~~~~~~ bSumEkinhOld); ~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:53: /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:544:31: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 dd_collect_vec(cr->dd, state, flocal, ftemp); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:554:45: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mimicCommunicator.sendForces(ftemp, state_global->natoms); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp:569:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 sum_dhdl(enerd, state->lambda, ir->fepvals); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_cg()': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &state->s, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->f); ~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_steep()': /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ top_global, step, static_cast(step), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &state->s, state_global, observablesHistory, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state->f); ~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/handlerestart.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/mdmodules.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp:55: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.h:50, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:46: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.h:50, from /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:46: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector*, gmx::PinningPolicy) [with T = gmx::BasicVector]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp:55: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_tpi()': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp:647:21: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 do_force(fplog, cr, ms, inputrec, nullptr, nullptr, ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ step, nrnb, wcycle, top, &top_global->groups, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_global->box, state_global->x.arrayRefWithPadding(), &state_global->hist, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ state_global->lambda, ~~~~~~~~~~~~~~~~~~~~~ nullptr, fr, ppForceWorkload, nullptr, mu_tot, t, nullptr, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS : 0) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (bStateChanged ? GMX_FORCE_STATECHANGED : 0), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdOpenBalanceRegionBeforeForceComputation::no, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DdCloseBalanceRegionAfterForceComputation::no); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp: In member function 'int gmx::Mdrunner::mdrunner()': /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:913:43: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cr->dd = init_domain_decomposition(mdlog, cr, domdecOptions, mdrunOptions, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &mtop, inputrec, ~~~~~~~~~~~~~~~~ box, positionsFromStatePointer(globalState.get()), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &atomSets); ~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp:1269:38: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 constructVsitesGlobal(mtop, globalState->x); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractoption.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractsection.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/behaviorcollection.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/options.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsassigner.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsection.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsvisitor.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/timeunitmanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate::ValueList*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/treesupport.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/manager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = double]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate::addValue(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector::append(const T&) [with T = long long int]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:60, from /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.h:49, from /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.cpp:38: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr, const std::vector&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H 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make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 1%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend [ 3%] Built target tng_io_obj /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/external/googletest 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'/build/gromacs-2019.1/build/openmpi' [ 21%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend [ 22%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd 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/build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp Scanning dependencies of target gmock make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/external/googletest && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googlemock/src/gmock-all.cc /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 22%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 23%] Built target mdrunutility-test-shared cd /build/gromacs-2019.1/build/openmpi/src/external/googletest && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googletest/src/gtest-all.cc make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 80%] Built target libgromacs cd /build/gromacs-2019.1/build/openmpi/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/openmpi/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o /usr/bin/ranlib ../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 81%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/testutils /build/gromacs-2019.1/build/openmpi/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-2019.1/src/testutils/cmdlinetest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/gromacs-2019.1/src/testutils/conftest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/gromacs-2019.1/src/testutils/filematchers.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/interactivetest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/gromacs-2019.1/src/testutils/loggertest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpi-printer.cpp.o -c /build/gromacs-2019.1/src/testutils/mpi-printer.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/mpitest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata-xml.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata-xml.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/gromacs-2019.1/src/testutils/stdiohelper.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/gromacs-2019.1/src/testutils/stringtest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/gromacs-2019.1/src/testutils/testasserts.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/gromacs-2019.1/src/testutils/testfilemanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/gromacs-2019.1/src/testutils/testfileredirector.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/gromacs-2019.1/src/testutils/testinit.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/testmatchers.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/gromacs-2019.1/src/testutils/testoptions.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/textblockmatchers.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/gromacs-2019.1/src/testutils/xvgtest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/gromacs-2019.1/src/external/tinyxml2/tinyxml2.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi-printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata-xml.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 83%] Built target testutils /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/testutils/tests /build/gromacs-2019.1/build/openmpi/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/compat/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/testutils/tests /build/gromacs-2019.1/build/openmpi/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build Scanning dependencies of target testutils-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/make_unique.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/mpitest.cpp Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/interactivetest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/refdata_tests.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 83%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 84%] Built target compat-test /usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target applied-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/mdebin.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/testasserts_tests.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 84%] Built target applied-forces-test /usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target listed-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/tests/bonded.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 85%] Built target testutils-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/commandline/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 85%] Built target listed-forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/domdec/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/hashedmap.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 85%] Built target domdec-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/ewald/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 86%] Built target mdlib-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fft/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 87%] Built target fft-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/pargs.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 88%] Built target commandline-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/hardware/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 88%] Built target hardware-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/math/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 88%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 89%] Built target ewald-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/math/arrayrefwithpadding.h:49, from /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp:43: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/math/arrayrefwithpadding.h:49, from /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 89%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 89%] Built target mdrunutility-mpi-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/options/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpmanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp:49: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 90%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/random/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoption.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp In file included from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:59: /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef >, int) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void fillInputContents(ArrayRef < BasicVector < T>> inputRef, ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoptionmanager.cpp /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void compareViews(ArrayRef input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef >, gmx::ArrayRef >) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void compareViews(ArrayRef < BasicVector < T>> input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector, gmx::Allocator, gmx::AlignedAllocationPolicy> >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/option.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector, std::allocator > >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/seed.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm In file included from /usr/include/c++/8/vector:64, from /usr/include/c++/8/bits/random.h:34, from /usr/include/c++/8/random:49, from /build/gromacs-2019.1/src/gromacs/random/seed.h:51, from /build/gromacs-2019.1/src/gromacs/random/threefry.h:51, from /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 vector(initializer_list __l, ^~~~~~ make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 90%] Built target math-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/restraint/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/repeatingsection.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 91%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tables/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformintdistribution.cpp /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}}, ^~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/timeunitmanager.cpp /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}}, ^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 92%] Built target random-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 92%] Built target table-test cd /build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 93%] Built target taskassignment-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 94%] Built target options-test cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 95%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fileio/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask64.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 95%] Built target fileio-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/pulling/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask128.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 95%] Built target pull-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/awh/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.h:57, from /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 95%] Built target awh-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/simd/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/gmxregex.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/base.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/path.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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/build/gromacs-2019.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && 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-DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" 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/build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 97%] Built target utility-test cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [100%] Built target simd-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1 /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[1]: Leaving directory '/build/gromacs-2019.1/build/openmpi' (cd build/openmpi ; LD_LIBRARY_PATH=/build/gromacs-2019.1/build/openmpi/lib \ OMPI_MCA_plm_rsh_agent=/bin/false \ OMPI_MCA_rmaps_base_oversubscribe=1 \ ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 ) UpdateCTestConfiguration from :/build/gromacs-2019.1/build/openmpi/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/openmpi/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-2019.1/build/openmpi/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/openmpi/DartConfiguration.tcl Test project /build/gromacs-2019.1/build/openmpi Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/gromacs-2019.1/build/openmpi/bin/testutils-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (8 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (5 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (4 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (24 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (5 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariants 1: [ OK ] ReferenceDataTest.HandlesVariants (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (5 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms) 1: [----------] 34 tests from ReferenceDataTest (30 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (1 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (5 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (1 ms) 1: [----------] 4 tests from XvgTests (8 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (62 ms total) 1: [ PASSED ] 59 tests. 1/27 Test #1: TestUtilsUnitTests ............... Passed 2.02 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /usr/bin/mpiexec.openmpi "-np" "2" "/build/gromacs-2019.1/build/openmpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (3 ms) 2: [----------] 1 test from MpiSelfTest (3 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (3 ms total) 2: [ PASSED ] 1 test. 2/27 Test #2: TestUtilsMpiUnitTests ............ Passed 0.67 sec test 3 Start 3: MdlibUnitTest 3: Test command: /build/gromacs-2019.1/build/openmpi/bin/mdlib-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/MdlibUnitTest.xml" 3: Test timeout computed to be: 30 3: [==========] Running 50 tests from 8 test cases. 3: [----------] Global test environment set-up. 3: [----------] 1 test from VerletBufferConstraintTest 3: [ RUN ] VerletBufferConstraintTest.EqualMasses 3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 3: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 3: 3: [----------] 3 tests from PrintEbin 3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (28 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (1 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (1 ms) 3: [----------] 3 tests from PrintEbin (30 ms total) 3: 3: [----------] 4 tests from ShakeTest 3: [ RUN ] ShakeTest.ConstrainsOneBond 3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 3: [----------] 4 tests from ShakeTest (0 ms total) 3: 3: [----------] 1 test from NullSignalTest 3: [ RUN ] NullSignalTest.NullSignallerWorks 3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 3: [----------] 1 test from NullSignalTest (0 ms total) 3: 3: [----------] 7 tests from SignalTest 3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 3: [----------] 7 tests from SignalTest (1 ms total) 3: 3: [----------] 9 tests from UpdateGroups 3: [ RUN ] UpdateGroups.ethaneUA 3: [ OK ] UpdateGroups.ethaneUA (4 ms) 3: [ RUN ] UpdateGroups.methane 3: [ OK ] UpdateGroups.methane (0 ms) 3: [ RUN ] UpdateGroups.ethane 3: [ OK ] UpdateGroups.ethane (0 ms) 3: [ RUN ] UpdateGroups.butaneUA 3: [ OK ] UpdateGroups.butaneUA (0 ms) 3: [ RUN ] UpdateGroups.waterThreeSite 3: [ OK ] UpdateGroups.waterThreeSite (1 ms) 3: [ RUN ] UpdateGroups.waterFourSite 3: [ OK ] UpdateGroups.waterFourSite (0 ms) 3: [ RUN ] UpdateGroups.fourAtomsWithSettle 3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 3: [ RUN ] UpdateGroups.waterFlexAngle 3: [ OK ] UpdateGroups.waterFlexAngle (18 ms) 3: [ RUN ] UpdateGroups.twoMoltypes 3: [ OK ] UpdateGroups.twoMoltypes (0 ms) 3: [----------] 9 tests from UpdateGroups (25 ms total) 3: 3: [----------] 1 test from UpdateGroupsCog 3: [ RUN ] UpdateGroupsCog.ComputesCogs 3: [ OK ] UpdateGroupsCog.ComputesCogs (2 ms) 3: [----------] 1 test from UpdateGroupsCog (2 ms total) 3: 3: [----------] 24 tests from WithParameters/SettleTest 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (1 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms) 3: [----------] 24 tests from WithParameters/SettleTest (2 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 50 tests from 8 test cases ran. (60 ms total) 3: [ PASSED ] 50 tests. 3/27 Test #3: MdlibUnitTest .................... Passed 0.76 sec test 4 Start 4: AppliedForcesUnitTest 4: Test command: /build/gromacs-2019.1/build/openmpi/bin/applied-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/AppliedForcesUnitTest.xml" 4: Test timeout computed to be: 30 4: [==========] Running 3 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 3 tests from ElectricFieldTest 4: [ RUN ] ElectricFieldTest.Static 4: [ OK ] ElectricFieldTest.Static (0 ms) 4: [ RUN ] ElectricFieldTest.Oscillating 4: [ OK ] ElectricFieldTest.Oscillating (0 ms) 4: [ RUN ] ElectricFieldTest.Pulsed 4: [ OK ] ElectricFieldTest.Pulsed (0 ms) 4: [----------] 3 tests from ElectricFieldTest (0 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 3 tests from 1 test case ran. (0 ms total) 4: [ PASSED ] 3 tests. 4/27 Test #4: AppliedForcesUnitTest ............ Passed 0.65 sec test 5 Start 5: ListedForcesTest 5: Test command: /build/gromacs-2019.1/build/openmpi/bin/listed-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/ListedForcesTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 15 tests from 1 test case. 5: [----------] Global test environment set-up. 5: [----------] 15 tests from BondedTest 5: [ RUN ] BondedTest.BondAnglePbcNone 5: [ OK ] BondedTest.BondAnglePbcNone (11 ms) 5: [ RUN ] BondedTest.BondAnglePbcXy 5: [ OK ] BondedTest.BondAnglePbcXy (1 ms) 5: [ RUN ] BondedTest.BondAnglePbcXyz 5: [ OK ] BondedTest.BondAnglePbcXyz (6 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcNone 5: [ OK ] BondedTest.DihedralAnglePbcNone (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXy 5: [ OK ] BondedTest.DihedralAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXyz 5: [ OK ] BondedTest.DihedralAnglePbcXyz (1 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcNo 5: [ OK ] BondedTest.IfuncBondsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXy 5: [ OK ] BondedTest.IfuncBondsPbcXy (1 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXyz 5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcNo 5: [ OK ] BondedTest.IfuncAnglesPbcNo (1 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXy 5: [ OK ] BondedTest.IfuncAnglesPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ 5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (1 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo 5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (6 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms) 5: [----------] 15 tests from BondedTest (31 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 15 tests from 1 test case ran. (32 ms total) 5: [ PASSED ] 15 tests. 5/27 Test #5: ListedForcesTest ................. Passed 0.80 sec test 6 Start 6: CommandLineUnitTests 6: Test command: /build/gromacs-2019.1/build/openmpi/bin/commandline-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/CommandLineUnitTests.xml" 6: Test timeout computed to be: 30 6: [==========] Running 55 tests from 6 test cases. 6: [----------] Global test environment set-up. 6: [----------] 3 tests from CommandLineHelpModuleTest 6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (16 ms) 6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (8 ms) 6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (3 ms) 6: [----------] 3 tests from CommandLineHelpModuleTest (27 ms total) 6: 6: [----------] 6 tests from CommandLineHelpWriterTest 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (5 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (6 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 6: [----------] 6 tests from CommandLineHelpWriterTest (14 ms total) 6: 6: [----------] 6 tests from CommandLineModuleManagerTest 6: [ RUN ] CommandLineModuleManagerTest.RunsModule 6: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 6: [----------] 6 tests from CommandLineModuleManagerTest (2 ms total) 6: 6: [----------] 13 tests from CommandLineParserTest 6: [ RUN ] CommandLineParserTest.HandlesSingleValues 6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms) 6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesString 6: [ OK ] CommandLineParserTest.HandlesString (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 6: [----------] 13 tests from CommandLineParserTest (1 ms total) 6: 6: [----------] 6 tests from CommandLineProgramContextTest 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (15 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (1 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 6: [----------] 6 tests from CommandLineProgramContextTest (16 ms total) 6: 6: [----------] 21 tests from ParseCommonArgsTest 6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (1 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (6 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (7 ms) 6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 6: [----------] 21 tests from ParseCommonArgsTest (16 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 55 tests from 6 test cases ran. (76 ms total) 6: [ PASSED ] 55 tests. 6/27 Test #6: CommandLineUnitTests ............. Passed 0.76 sec test 7 Start 7: DomDecTests 7: Test command: /build/gromacs-2019.1/build/openmpi/bin/domdec-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/DomDecTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 9 tests from 2 test cases. 7: [----------] Global test environment set-up. 7: [----------] 7 tests from HashedMap 7: [ RUN ] HashedMap.InsertsFinds 7: [ OK ] HashedMap.InsertsFinds (0 ms) 7: [ RUN ] HashedMap.NegativeKeysWork 7: [ OK ] HashedMap.NegativeKeysWork (0 ms) 7: [ RUN ] HashedMap.InsertsErases 7: [ OK ] HashedMap.InsertsErases (0 ms) 7: [ RUN ] HashedMap.InsertsOrAssigns 7: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 7: [ RUN ] HashedMap.Clears 7: [ OK ] HashedMap.Clears (0 ms) 7: [ RUN ] HashedMap.LinkedEntries 7: [ OK ] HashedMap.LinkedEntries (0 ms) 7: [ RUN ] HashedMap.ResizesTable 7: [ OK ] HashedMap.ResizesTable (0 ms) 7: [----------] 7 tests from HashedMap (0 ms total) 7: 7: [----------] 2 tests from LocalAtomSetManager 7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 7: [----------] 2 tests from LocalAtomSetManager (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 9 tests from 2 test cases ran. (1 ms total) 7: [ PASSED ] 9 tests. 7/27 Test #7: DomDecTests ...................... Passed 0.75 sec test 8 Start 8: EwaldUnitTests 8: Test command: /build/gromacs-2019.1/build/openmpi/bin/ewald-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/EwaldUnitTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 257 tests from 10 test cases. 8: [----------] Global test environment set-up. 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (55 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms) 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (56 ms total) 8: 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (35 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (40 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (14 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (12 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (12 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (8 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (8 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (12 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (12 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (8 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (8 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (8 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (28 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (9 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (10 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (10 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (9 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (12 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (8 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (12 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (12 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (8 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (16 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (14 ms) 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (327 ms total) 8: 8: [----------] 144 tests from SaneInput/PmeGatherTest 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (5 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (7 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (6 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (5 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (6 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (7 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (5 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (6 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (6 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (3 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (5 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (7 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (4 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (4 ms) 8: [----------] 144 tests from SaneInput/PmeGatherTest (309 ms total) 8: 8: [----------] 16 tests from SaneInput/PmeSolveTest 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (4 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (10 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (9 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (9 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (9 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (4 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (8 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (9 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (6 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (9 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (7 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (9 ms) 8: [----------] 16 tests from SaneInput/PmeSolveTest (110 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (8 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (8 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (7 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (8 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (9 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (8 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (7 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (8 ms) 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (63 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (10 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (8 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (7 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (8 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (9 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (8 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (7 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (8 ms) 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (65 ms total) 8: 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (8 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (9 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (7 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (9 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (6 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (9 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (7 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (9 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (8 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (9 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (7 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (9 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (5 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (9 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (7 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (9 ms) 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (128 ms total) 8: 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (8 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (12 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (8 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (9 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (8 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (9 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (6 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (8 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (8 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (9 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (9 ms) 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (102 ms total) 8: 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (6 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (8 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (8 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (8 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (8 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (9 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (9 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (9 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (8 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (8 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (11 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (19 ms) 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (114 ms total) 8: 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (25 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (16 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (22 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (29 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (39 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (36 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (24 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (20 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (22 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (37 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (53 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (37 ms) 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (393 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 257 tests from 10 test cases ran. (1707 ms total) 8: [ PASSED ] 257 tests. 8/27 Test #8: EwaldUnitTests ................... Passed 2.40 sec test 9 Start 9: FFTUnitTests 9: Test command: /build/gromacs-2019.1/build/openmpi/bin/fft-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/FFTUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 14 tests from 4 test cases. 9: [----------] Global test environment set-up. 9: [----------] 2 tests from ManyFFTTest 9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (46 ms) 9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (39 ms) 9: [----------] 2 tests from ManyFFTTest (92 ms total) 9: 9: [----------] 1 test from FFTTest 9: [ RUN ] FFTTest.Real2DLength18_15Test 9: [ OK ] FFTTest.Real2DLength18_15Test (28 ms) 9: [----------] 1 test from FFTTest (29 ms total) 9: 9: [----------] 1 test from FFFTest3D 9: [ RUN ] FFFTest3D.Real5_6_9 9: [ OK ] FFFTest3D.Real5_6_9 (15 ms) 9: [----------] 1 test from FFFTest3D (16 ms total) 9: 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (8 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (3 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (11 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (5 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (14 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (20 ms) 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (70 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 14 tests from 4 test cases ran. (208 ms total) 9: [ PASSED ] 14 tests. 9/27 Test #9: FFTUnitTests ..................... Passed 0.84 sec test 10 Start 10: GpuUtilsUnitTests 10: Test command: /build/gromacs-2019.1/build/openmpi/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/GpuUtilsUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 60 tests from 19 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (1 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Swap 10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Comparison 10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Swap 10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Comparison 10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Swap 10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Comparison 10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Swap 10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Comparison 10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 10: 10: [----------] 1 test from HostAllocatorUntypedTest 10: [ RUN ] HostAllocatorUntypedTest.Comparison 10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.Move 10: [ OK ] AllocatorTest/0.Move (1 ms) 10: [----------] 4 tests from AllocatorTest/0 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.Move 10: [ OK ] AllocatorTest/1.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/1 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.Move 10: [ OK ] AllocatorTest/2.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/2 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.Move 10: [ OK ] AllocatorTest/3.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/3 (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 60 tests from 19 test cases ran. (2 ms total) 10: [ PASSED ] 60 tests. 10/27 Test #10: GpuUtilsUnitTests ................ Passed 0.65 sec test 11 Start 11: HardwareUnitTests 11: Test command: /build/gromacs-2019.1/build/openmpi/bin/hardware-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/HardwareUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 4 tests from 1 test case. 11: [----------] Global test environment set-up. 11: [----------] 4 tests from HardwareTopologyTest 11: [ RUN ] HardwareTopologyTest.Execute 11: [ OK ] HardwareTopologyTest.Execute (17 ms) 11: [ RUN ] HardwareTopologyTest.HwlocExecute 11: [ OK ] HardwareTopologyTest.HwlocExecute (17 ms) 11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (17 ms) 11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (17 ms) 11: [----------] 4 tests from HardwareTopologyTest (69 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 4 tests from 1 test case ran. (69 ms total) 11: [ PASSED ] 4 tests. 11/27 Test #11: HardwareUnitTests ................ Passed 1.08 sec test 12 Start 12: MathUnitTests 12: Test command: /build/gromacs-2019.1/build/openmpi/bin/math-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/MathUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 112 tests from 20 test cases. 12: [----------] Global test environment set-up. 12: [----------] 1 test from EmptyArrayRefWithPaddingTest 12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 12: 12: [----------] 6 tests from StructureSimilarityTest 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 12: [----------] 6 tests from StructureSimilarityTest (0 ms total) 12: 12: [----------] 21 tests from FunctionTest 12: [ RUN ] FunctionTest.StaticLog2 12: [ OK ] FunctionTest.StaticLog2 (23 ms) 12: [ RUN ] FunctionTest.Log2I32Bit 12: [ OK ] FunctionTest.Log2I32Bit (0 ms) 12: [ RUN ] FunctionTest.Log2I64Bit 12: [ OK ] FunctionTest.Log2I64Bit (7 ms) 12: [ RUN ] FunctionTest.GreatestCommonDivisor 12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 12: [ RUN ] FunctionTest.InvsqrtFloat 12: [ OK ] FunctionTest.InvsqrtFloat (1 ms) 12: [ RUN ] FunctionTest.InvsqrtDouble 12: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvsqrtInteger 12: [ OK ] FunctionTest.InvsqrtInteger (1 ms) 12: [ RUN ] FunctionTest.InvcbrtFloat 12: [ OK ] FunctionTest.InvcbrtFloat (1 ms) 12: [ RUN ] FunctionTest.InvcbrtDouble 12: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvcbrtInteger 12: [ OK ] FunctionTest.InvcbrtInteger (1 ms) 12: [ RUN ] FunctionTest.SixthrootFloat 12: [ OK ] FunctionTest.SixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.SixthrootDouble 12: [ OK ] FunctionTest.SixthrootDouble (1 ms) 12: [ RUN ] FunctionTest.SixthrootInteger 12: [ OK ] FunctionTest.SixthrootInteger (1 ms) 12: [ RUN ] FunctionTest.InvsixthrootFloat 12: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootDouble 12: [ OK ] FunctionTest.InvsixthrootDouble (1 ms) 12: [ RUN ] FunctionTest.InvsixthrootInteger 12: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.Powers 12: [ OK ] FunctionTest.Powers (0 ms) 12: [ RUN ] FunctionTest.ErfInvFloat 12: [ OK ] FunctionTest.ErfInvFloat (1 ms) 12: [ RUN ] FunctionTest.ErfInvDouble 12: [ OK ] FunctionTest.ErfInvDouble (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 12: [----------] 21 tests from FunctionTest (40 ms total) 12: 12: [----------] 2 tests from InvertMatrixTest 12: [ RUN ] InvertMatrixTest.IdentityIsImpotent 12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertMatrixTest.ComputesInverse 12: [ OK ] InvertMatrixTest.ComputesInverse (1 ms) 12: [----------] 2 tests from InvertMatrixTest (1 ms total) 12: 12: [----------] 2 tests from InvertBoxMatrixTest 12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanCopyAssign 12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanMoveAssign 12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanSwap 12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanCopyAssign 12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanMoveAssign 12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanSwap 12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanCopyAssign 12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanMoveAssign 12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanSwap 12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanCopyAssign 12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanMoveAssign 12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanSwap 12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanCopyAssign 12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanMoveAssign 12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanSwap 12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanCopyAssign 12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanMoveAssign 12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanSwap 12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanCopyAssign 12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanMoveAssign 12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanSwap 12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/6 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanCopyAssign 12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanMoveAssign 12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanSwap 12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanCopyAssign 12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanMoveAssign 12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanSwap 12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanCopyAssign 12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanMoveAssign 12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanSwap 12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 12: 12: [----------] 33 tests from RVecTest 12: [ RUN ] RVecTest.CanBeStoredInVector 12: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAsMutable_rvec 12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Array 12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 12: [ RUN ] RVecTest.CanAddRVecToRvec 12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanAddAssignRVecToRvec 12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractRVecFromRvec 12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanDotProductRVecByRvec 12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanCrossProductRVecByRvec 12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVecInplace 12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 12: [ RUN ] RVecTest.CanScaleRVec 12: [ OK ] RVecTest.CanScaleRVec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVec 12: [ OK ] RVecTest.CanDivideRVec (0 ms) 12: [ RUN ] RVecTest.CanDoUnitvFromRVec 12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanSqLengthOfRVec 12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanLengthOfRVec 12: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToRVec 12: [ OK ] RVecTest.CanCastToRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToDVec 12: [ OK ] RVecTest.CanCastToDVec (0 ms) 12: [ RUN ] RVecTest.CanLeftScalarMultiply 12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanRightScalarMultiply 12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanGetUnitvFromRVec 12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanGetSqLengthOfRVec 12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanGetLengthOfRVec 12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoCrossProductOfRVec 12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoDotProductOfRVec 12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 12: [ RUN ] RVecTest.WorksAs_dvec_Reference 12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_ivec_Reference 12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Reference 12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 12: [ RUN ] RVecTest.CopyConstructorWorks 12: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 12: [ RUN ] RVecTest.CopyAssignmentWorks 12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 12: [ RUN ] RVecTest.MoveConstructorWorks 12: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 12: [ RUN ] RVecTest.MoveAssignmentWorks 12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 12: [----------] 33 tests from RVecTest (9 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 112 tests from 20 test cases ran. (52 ms total) 12: [ PASSED ] 112 tests. 12/27 Test #12: MathUnitTests .................... Passed 0.69 sec test 13 Start 13: MdrunUtilityUnitTests 13: Test command: /build/gromacs-2019.1/build/openmpi/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/MdrunUtilityUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 17 tests from 1 test case. 13: [----------] Global test environment set-up. 13: [----------] 17 tests from ThreadAffinityTest 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 13: NOTE: Affinity setting failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (10 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (8 ms) 13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (8 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 13: NOTE: Affinity setting for 1/2 threads failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (4 ms) 13: [----------] 17 tests from ThreadAffinityTest (36 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 17 tests from 1 test case ran. (36 ms total) 13: [ PASSED ] 17 tests. 13/27 Test #13: MdrunUtilityUnitTests ............ Passed 0.67 sec test 14 Start 14: MdrunUtilityMpiUnitTests 14: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "/build/gromacs-2019.1/build/openmpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 13 tests from 2 test cases. 14: [----------] Global test environment set-up. 14: [----------] 6 tests from ThreadAffinityMultiRankTest 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (71 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (72 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (57 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (43 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (48 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (8 ms) 14: [----------] 6 tests from ThreadAffinityMultiRankTest (347 ms total) 14: 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (80 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (28 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (4 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (1 ms) 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (137 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 13 tests from 2 test cases ran. (486 ms total) 14: [ PASSED ] 13 tests. 14/27 Test #14: MdrunUtilityMpiUnitTests ......... Passed 1.33 sec test 15 Start 15: OnlineHelpUnitTests 15: Test command: /build/gromacs-2019.1/build/openmpi/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/OnlineHelpUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 22 tests from 4 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from TextTableFormatterTest 15: [ RUN ] TextTableFormatterTest.HandlesBasicCase 15: [ OK ] TextTableFormatterTest.HandlesBasicCase (32 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (4 ms) 15: [ RUN ] TextTableFormatterTest.HandlesIndentation 15: [ OK ] TextTableFormatterTest.HandlesIndentation (4 ms) 15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (4 ms) 15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (4 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (4 ms) 15: [----------] 6 tests from TextTableFormatterTest (52 ms total) 15: 15: [----------] 3 tests from HelpManagerTest 15: [ RUN ] HelpManagerTest.HandlesRootTopic 15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 15: [ RUN ] HelpManagerTest.HandlesSubTopics 15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 15: [ RUN ] HelpManagerTest.HandlesInvalidTopics 15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 15: [----------] 3 tests from HelpManagerTest (0 ms total) 15: 15: [----------] 2 tests from HelpTopicFormattingTest 15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (4 ms) 15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (4 ms) 15: [----------] 2 tests from HelpTopicFormattingTest (8 ms total) 15: 15: [----------] 11 tests from HelpWriterContextTest 15: [ RUN ] HelpWriterContextTest.FormatsParagraphs 15: [ OK ] HelpWriterContextTest.FormatsParagraphs (4 ms) 15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (4 ms) 15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (4 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralText 15: [ OK ] HelpWriterContextTest.FormatsLiteralText (4 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (4 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (4 ms) 15: [ RUN ] HelpWriterContextTest.FormatsBulletList 15: [ OK ] HelpWriterContextTest.FormatsBulletList (4 ms) 15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (4 ms) 15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (4 ms) 15: [ RUN ] HelpWriterContextTest.FormatsGridTable 15: [ OK ] HelpWriterContextTest.FormatsGridTable (4 ms) 15: [ RUN ] HelpWriterContextTest.FormatsTitles 15: [ OK ] HelpWriterContextTest.FormatsTitles (4 ms) 15: [----------] 11 tests from HelpWriterContextTest (44 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 22 tests from 4 test cases ran. (104 ms total) 15: [ PASSED ] 22 tests. 15/27 Test #15: OnlineHelpUnitTests .............. Passed 0.68 sec test 16 Start 16: OptionsUnitTests 16: Test command: /build/gromacs-2019.1/build/openmpi/bin/options-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/OptionsUnitTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 110 tests from 18 test cases. 16: [----------] Global test environment set-up. 16: [----------] 5 tests from AbstractOptionStorageTest 16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 16: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 16: 16: [----------] 8 tests from FileNameOptionTest 16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (1 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 16: [----------] 8 tests from FileNameOptionTest (1 ms total) 16: 16: [----------] 15 tests from FileNameOptionManagerTest 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 16: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 16: 16: [----------] 1 test from OptionsTest 16: [ RUN ] OptionsTest.FailsOnNonsafeStorage 16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 16: [----------] 1 test from OptionsTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerTest 16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMissingValue 16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesExtraValue 16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesGroups 16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesSections 16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 16: [----------] 9 tests from OptionsAssignerTest (0 ms total) 16: 16: [----------] 4 tests from OptionsAssignerBooleanTest 16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 16: 16: [----------] 13 tests from OptionsAssignerIntegerTest 16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (4 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (1 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 16: [----------] 13 tests from OptionsAssignerIntegerTest (5 ms total) 16: 16: [----------] 5 tests from OptionsAssignerDoubleTest 16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 16: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerStringTest 16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 9 tests from OptionsAssignerStringTest (1 ms total) 16: 16: [----------] 6 tests from OptionsAssignerEnumTest 16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 16: 16: [----------] 8 tests from RepeatingOptionSectionTest 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 16: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 16: 16: [----------] 1 test from TimeUnitManagerTest 16: [ RUN ] TimeUnitManagerTest.BasicOperations 16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 16: [----------] 1 test from TimeUnitManagerTest (0 ms total) 16: 16: [----------] 4 tests from TimeUnitBehaviorTest 16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 16: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 16: 16: [----------] 2 tests from TreeValueSupportAssignTest 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (1 ms) 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 16: [----------] 2 tests from TreeValueSupportAssignTest (1 ms total) 16: 16: [----------] 1 test from TreeValueSupportAssignErrorTest 16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 16: 16: [----------] 5 tests from TreeValueSupportCheckTest 16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 16: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 16: 16: [----------] 6 tests from TreeValueSupportAdjustTest 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (30 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (1 ms) 16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (6 ms) 16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 16: [----------] 6 tests from TreeValueSupportAdjustTest (38 ms total) 16: 16: [----------] 8 tests from TreeValueSupportTest 16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsInt64Option 16: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsStringOption 16: [ OK ] TreeValueSupportTest.SupportsStringOption (6 ms) 16: [ RUN ] TreeValueSupportTest.SupportsFloatOption 16: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumOption 16: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 16: [----------] 8 tests from TreeValueSupportTest (10 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 110 tests from 18 test cases ran. (58 ms total) 16: [ PASSED ] 110 tests. 16/27 Test #16: OptionsUnitTests ................. Passed 0.67 sec test 17 Start 17: RandomUnitTests 17: Test command: /build/gromacs-2019.1/build/openmpi/bin/random-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/RandomUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 44 tests from 10 test cases. 17: [----------] Global test environment set-up. 17: [----------] 4 tests from ExponentialDistributionTest 17: [ RUN ] ExponentialDistributionTest.Output 17: [ OK ] ExponentialDistributionTest.Output (8 ms) 17: [ RUN ] ExponentialDistributionTest.Logical 17: [ OK ] ExponentialDistributionTest.Logical (0 ms) 17: [ RUN ] ExponentialDistributionTest.Reset 17: [ OK ] ExponentialDistributionTest.Reset (0 ms) 17: [ RUN ] ExponentialDistributionTest.AltParam 17: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from ExponentialDistributionTest (8 ms total) 17: 17: [----------] 4 tests from GammaDistributionTest 17: [ RUN ] GammaDistributionTest.Output 17: [ OK ] GammaDistributionTest.Output (1 ms) 17: [ RUN ] GammaDistributionTest.Logical 17: [ OK ] GammaDistributionTest.Logical (0 ms) 17: [ RUN ] GammaDistributionTest.Reset 17: [ OK ] GammaDistributionTest.Reset (0 ms) 17: [ RUN ] GammaDistributionTest.AltParam 17: [ OK ] GammaDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from GammaDistributionTest (1 ms total) 17: 17: [----------] 4 tests from NormalDistributionTest 17: [ RUN ] NormalDistributionTest.Output 17: [ OK ] NormalDistributionTest.Output (1 ms) 17: [ RUN ] NormalDistributionTest.Logical 17: [ OK ] NormalDistributionTest.Logical (0 ms) 17: [ RUN ] NormalDistributionTest.Reset 17: [ OK ] NormalDistributionTest.Reset (0 ms) 17: [ RUN ] NormalDistributionTest.AltParam 17: [ OK ] NormalDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from NormalDistributionTest (1 ms total) 17: 17: [----------] 1 test from SeedTest 17: [ RUN ] SeedTest.makeRandomSeed 17: [ OK ] SeedTest.makeRandomSeed (0 ms) 17: [----------] 1 test from SeedTest (0 ms total) 17: 17: [----------] 6 tests from TabulatedNormalDistributionTest 17: [ RUN ] TabulatedNormalDistributionTest.Output14 17: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Output16 17: [ OK ] TabulatedNormalDistributionTest.Output16 (5 ms) 17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Logical 17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Reset 17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.AltParam 17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 17: [----------] 6 tests from TabulatedNormalDistributionTest (6 ms total) 17: 17: [----------] 1 test from TabulatedNormalDistributionTableTest 17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (5 ms) 17: [----------] 1 test from TabulatedNormalDistributionTableTest (5 ms total) 17: 17: [----------] 6 tests from ThreeFry2x64Test 17: [ RUN ] ThreeFry2x64Test.Logical 17: [ OK ] ThreeFry2x64Test.Logical (0 ms) 17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (6 ms) 17: [ RUN ] ThreeFry2x64Test.Reseed 17: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 17: [ RUN ] ThreeFry2x64Test.Discard 17: [ OK ] ThreeFry2x64Test.Discard (0 ms) 17: [ RUN ] ThreeFry2x64Test.InvalidCounter 17: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 17: [----------] 6 tests from ThreeFry2x64Test (7 ms total) 17: 17: [----------] 4 tests from UniformIntDistributionTest 17: [ RUN ] UniformIntDistributionTest.Output 17: [ OK ] UniformIntDistributionTest.Output (1 ms) 17: [ RUN ] UniformIntDistributionTest.Logical 17: [ OK ] UniformIntDistributionTest.Logical (0 ms) 17: [ RUN ] UniformIntDistributionTest.Reset 17: [ OK ] UniformIntDistributionTest.Reset (0 ms) 17: [ RUN ] UniformIntDistributionTest.AltParam 17: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from UniformIntDistributionTest (1 ms total) 17: 17: [----------] 5 tests from UniformRealDistributionTest 17: [ RUN ] UniformRealDistributionTest.GenerateCanonical 17: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms) 17: [ RUN ] UniformRealDistributionTest.Output 17: [ OK ] UniformRealDistributionTest.Output (0 ms) 17: [ RUN ] UniformRealDistributionTest.Logical 17: [ OK ] UniformRealDistributionTest.Logical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Reset 17: [ OK ] UniformRealDistributionTest.Reset (0 ms) 17: [ RUN ] UniformRealDistributionTest.AltParam 17: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 17: [----------] 5 tests from UniformRealDistributionTest (2 ms total) 17: 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (1 ms) 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (4 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 44 tests from 10 test cases ran. (35 ms total) 17: [ PASSED ] 44 tests. 17/27 Test #17: RandomUnitTests .................. Passed 0.73 sec test 18 Start 18: RestraintTests 18: Test command: /build/gromacs-2019.1/build/openmpi/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/RestraintTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 1 test from 1 test case. 18: [----------] Global test environment set-up. 18: [----------] 1 test from RestraintManager 18: [ RUN ] RestraintManager.restraintList 18: [ OK ] RestraintManager.restraintList (0 ms) 18: [----------] 1 test from RestraintManager (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1 test from 1 test case ran. (0 ms total) 18: [ PASSED ] 1 test. 18/27 Test #18: RestraintTests ................... Passed 0.68 sec test 19 Start 19: TableUnitTests 19: Test command: /build/gromacs-2019.1/build/openmpi/bin/table-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/TableUnitTests.xml" 19: Test timeout computed to be: 30 19: [==========] Running 16 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (5 ms) 19: [ RUN ] SplineTableTest/0.Sinc 19: [ OK ] SplineTableTest/0.Sinc (2 ms) 19: [ RUN ] SplineTableTest/0.LJ12 19: [ OK ] SplineTableTest/0.LJ12 (114 ms) 19: [ RUN ] SplineTableTest/0.PmeCorrection 19: [ OK ] SplineTableTest/0.PmeCorrection (4 ms) 19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (12 ms) 19: [ RUN ] SplineTableTest/0.TwoFunctions 19: [ OK ] SplineTableTest/0.TwoFunctions (222 ms) 19: [ RUN ] SplineTableTest/0.ThreeFunctions 19: [ OK ] SplineTableTest/0.ThreeFunctions (134 ms) 19: [----------] 8 tests from SplineTableTest/0 (494 ms total) 19: 19: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (6 ms) 19: [ RUN ] SplineTableTest/1.Sinc 19: [ OK ] SplineTableTest/1.Sinc (2 ms) 19: [ RUN ] SplineTableTest/1.LJ12 19: [ OK ] SplineTableTest/1.LJ12 (10 ms) 19: [ RUN ] SplineTableTest/1.PmeCorrection 19: [ OK ] SplineTableTest/1.PmeCorrection (5 ms) 19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (4 ms) 19: [ RUN ] SplineTableTest/1.TwoFunctions 19: [ OK ] SplineTableTest/1.TwoFunctions (20 ms) 19: [ RUN ] SplineTableTest/1.ThreeFunctions 19: [ OK ] SplineTableTest/1.ThreeFunctions (22 ms) 19: [----------] 8 tests from SplineTableTest/1 (70 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 16 tests from 2 test cases ran. (564 ms total) 19: [ PASSED ] 16 tests. 19/27 Test #19: TableUnitTests ................... Passed 1.14 sec test 20 Start 20: TaskAssignmentUnitTests 20: Test command: /build/gromacs-2019.1/build/openmpi/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/TaskAssignmentUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 3 tests from 1 test case. 20: [----------] Global test environment set-up. 20: [----------] 3 tests from GpuIdStringHandlingTest 20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork 20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid 20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow 20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (0 ms) 20: [----------] 3 tests from GpuIdStringHandlingTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 3 tests from 1 test case ran. (1 ms total) 20: [ PASSED ] 3 tests. 20/27 Test #20: TaskAssignmentUnitTests .......... Passed 0.41 sec test 21 Start 21: UtilityUnitTests 21: Test command: /build/gromacs-2019.1/build/openmpi/bin/utility-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/UtilityUnitTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 325 tests from 52 test cases. 21: [----------] Global test environment set-up. 21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.Move 21: [ OK ] AllocatorTest/0.Move (0 ms) 21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/0 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.Move 21: [ OK ] AllocatorTest/1.Move (0 ms) 21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/1 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.Move 21: [ OK ] AllocatorTest/2.Move (0 ms) 21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/2 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.Move 21: [ OK ] AllocatorTest/3.Move (0 ms) 21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/3 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.Move 21: [ OK ] AllocatorTest/4.Move (0 ms) 21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/4 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.Move 21: [ OK ] AllocatorTest/5.Move (0 ms) 21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/5 (0 ms total) 21: 21: [----------] 1 test from AllocatorUntypedTest 21: [ RUN ] AllocatorUntypedTest.Comparison 21: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 21: [----------] 1 test from AllocatorUntypedTest (0 ms total) 21: 21: [----------] 1 test from EmptyArrayRefTest 21: [ RUN ] EmptyArrayRefTest.IsEmpty 21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyArrayRefTest (0 ms total) 21: 21: [----------] 1 test from EmptyConstArrayRefTest 21: [ RUN ] EmptyConstArrayRefTest.IsEmpty 21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/0 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/6 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/12 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/17 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 21: 21: [----------] 4 tests from KeyValueTreeSerializerTest 21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (29 ms) 21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (4 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (4 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (4 ms) 21: [----------] 4 tests from KeyValueTreeSerializerTest (41 ms total) 21: 21: [----------] 6 tests from TreeValueTransformTest 21: [ RUN ] TreeValueTransformTest.SimpleTransforms 21: [ OK ] TreeValueTransformTest.SimpleTransforms (4 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (4 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (4 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromString 21: [ OK ] TreeValueTransformTest.ObjectFromString (4 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (4 ms) 21: [ RUN ] TreeValueTransformTest.ScopedTransformRules 21: [ OK ] TreeValueTransformTest.ScopedTransformRules (4 ms) 21: [----------] 6 tests from TreeValueTransformTest (24 ms total) 21: 21: [----------] 1 test from TreeValueTransformErrorTest 21: [ RUN ] TreeValueTransformErrorTest.ConversionError 21: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 21: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 21: 21: [----------] 2 tests from RegexBasicTest 21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported 21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (1 ms) 21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported 21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (1 ms) 21: [----------] 2 tests from RegexBasicTest (2 ms total) 21: 21: [----------] 5 tests from LoggerTest 21: [ RUN ] LoggerTest.EmptyLoggerWorks 21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToStream 21: [ OK ] LoggerTest.LogsToStream (5 ms) 21: [ RUN ] LoggerTest.LogsToFile 21: [ OK ] LoggerTest.LogsToFile (8 ms) 21: [ RUN ] LoggerTest.LevelFilteringWorks 21: [ OK ] LoggerTest.LevelFilteringWorks (3 ms) 21: [ RUN ] LoggerTest.LogsToMultipleStreams 21: [ OK ] LoggerTest.LogsToMultipleStreams (7 ms) 21: [----------] 5 tests from LoggerTest (26 ms total) 21: 21: [----------] 4 tests from MutexBasicTest 21: [ RUN ] MutexBasicTest.CanBeMade 21: [ OK ] MutexBasicTest.CanBeMade (0 ms) 21: [ RUN ] MutexBasicTest.CanBeLocked 21: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeTryLocked 21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 21: [----------] 4 tests from MutexBasicTest (0 ms total) 21: 21: [----------] 3 tests from MutexTaskTest 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (11 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (12 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 21: [----------] 3 tests from MutexTaskTest (23 ms total) 21: 21: [----------] 4 tests from PathTest 21: [ RUN ] PathTest.StripSourcePrefixWorks 21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks 21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathWorks 21: [ OK ] PathTest.GetParentPathWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathAndBasenameWorks 21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms) 21: [----------] 4 tests from PathTest (1 ms total) 21: 21: [----------] 2 tests from PhysicalNodeCommunicatorTest 21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 21: 21: [----------] 7 tests from StringUtilityTest 21: [ RUN ] StringUtilityTest.StartsWith 21: [ OK ] StringUtilityTest.StartsWith (0 ms) 21: [ RUN ] StringUtilityTest.EndsWith 21: [ OK ] StringUtilityTest.EndsWith (0 ms) 21: [ RUN ] StringUtilityTest.StripSuffixIfPresent 21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 21: [ RUN ] StringUtilityTest.StripString 21: [ OK ] StringUtilityTest.StripString (0 ms) 21: [ RUN ] StringUtilityTest.SplitString 21: [ OK ] StringUtilityTest.SplitString (0 ms) 21: [ RUN ] StringUtilityTest.SplitDelimitedString 21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms) 21: [----------] 7 tests from StringUtilityTest (1 ms total) 21: 21: [----------] 2 tests from FormatStringTest 21: [ RUN ] FormatStringTest.HandlesBasicFormatting 21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 21: [ RUN ] FormatStringTest.HandlesLongStrings 21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 21: [----------] 2 tests from FormatStringTest (0 ms total) 21: 21: [----------] 1 test from StringFormatterTest 21: [ RUN ] StringFormatterTest.HandlesBasicFormatting 21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 21: [----------] 1 test from StringFormatterTest (0 ms total) 21: 21: [----------] 1 test from formatAndJoinTest 21: [ RUN ] formatAndJoinTest.Works 21: [ OK ] formatAndJoinTest.Works (0 ms) 21: [----------] 1 test from formatAndJoinTest (0 ms total) 21: 21: [----------] 1 test from JoinStringsTest 21: [ RUN ] JoinStringsTest.Works 21: [ OK ] JoinStringsTest.Works (0 ms) 21: [----------] 1 test from JoinStringsTest (0 ms total) 21: 21: [----------] 6 tests from ReplaceAllTest 21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesNoMatches 21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 21: [----------] 6 tests from ReplaceAllTest (0 ms total) 21: 21: [----------] 10 tests from TextLineWrapperTest 21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectly 21: [ OK ] TextLineWrapperTest.WrapsCorrectly (7 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (4 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndent 21: [ OK ] TextLineWrapperTest.HandlesIndent (4 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (3 ms) 21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (3 ms) 21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (3 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (4 ms) 21: [----------] 10 tests from TextLineWrapperTest (31 ms total) 21: 21: [----------] 6 tests from TextWriterTest 21: [ RUN ] TextWriterTest.WritesLines 21: [ OK ] TextWriterTest.WritesLines (3 ms) 21: [ RUN ] TextWriterTest.WritesLinesInParts 21: [ OK ] TextWriterTest.WritesLinesInParts (3 ms) 21: [ RUN ] TextWriterTest.WritesWrappedLines 21: [ OK ] TextWriterTest.WritesWrappedLines (3 ms) 21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (3 ms) 21: [ RUN ] TextWriterTest.TracksNewlines 21: [ OK ] TextWriterTest.TracksNewlines (3 ms) 21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (3 ms) 21: [----------] 6 tests from TextWriterTest (24 ms total) 21: 21: [----------] 1 test from TypeTraitsTest 21: [ RUN ] TypeTraitsTest.IsIntegralConstant 21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 21: [----------] 1 test from TypeTraitsTest (0 ms total) 21: 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 21: 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (11 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (13 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (11 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (12 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (12 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (12 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (72 ms total) 21: 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (1 ms) 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 325 tests from 52 test cases ran. (252 ms total) 21: [ PASSED ] 325 tests. 21/27 Test #21: UtilityUnitTests ................. Passed 0.85 sec test 22 Start 22: UtilityMpiUnitTests 22: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "/build/gromacs-2019.1/build/openmpi/bin/utility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/UtilityMpiUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 2 tests from 1 test case. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from PhysicalNodeCommunicatorTest 22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (36 ms) 22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (50 ms) 22: [----------] 2 tests from PhysicalNodeCommunicatorTest (113 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test case ran. (116 ms total) 22: [ PASSED ] 2 tests. 22/27 Test #22: UtilityMpiUnitTests .............. Passed 1.02 sec test 23 Start 23: FileIOTests 23: Test command: /build/gromacs-2019.1/build/openmpi/bin/fileio-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/FileIOTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 17 tests from 4 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from FileMD5Test 23: [ RUN ] FileMD5Test.CanComputeMD5 23: [ OK ] FileMD5Test.CanComputeMD5 (9 ms) 23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 23: [----------] 2 tests from FileMD5Test (10 ms total) 23: 23: [----------] 9 tests from ReadTest 23: [ RUN ] ReadTest.get_eint_ReadsInteger 23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_eint64_ReadsInteger 23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsInteger 23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsFloat 23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 23: [ RUN ] ReadTest.get_ereal_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not a 23: real value 23: 23: 23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 23: [----------] 9 tests from ReadTest (0 ms total) 23: 23: [----------] 2 tests from TngTest 23: [ RUN ] TngTest.CanOpenTngFile 23: [ OK ] TngTest.CanOpenTngFile (11 ms) 23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 23: [----------] 2 tests from TngTest (11 ms total) 23: 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (7 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (38 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (2 ms) 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (56 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 17 tests from 4 test cases ran. (77 ms total) 23: [ PASSED ] 17 tests. 23/27 Test #23: FileIOTests ...................... Passed 0.72 sec test 24 Start 24: PullTest 24: Test command: /build/gromacs-2019.1/build/openmpi/bin/pull-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/PullTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 5 tests from 1 test case. 24: [----------] Global test environment set-up. 24: [----------] 5 tests from PullTest 24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 24: [----------] 5 tests from PullTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 5 tests from 1 test case ran. (0 ms total) 24: [ PASSED ] 5 tests. 24/27 Test #24: PullTest ......................... Passed 0.39 sec test 25 Start 25: AwhTest 25: Test command: /build/gromacs-2019.1/build/openmpi/bin/awh-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/AwhTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 12 tests from 4 test cases. 25: [----------] Global test environment set-up. 25: [----------] 1 test from BiasTest 25: [ RUN ] BiasTest.DetectsCovering 25: [ OK ] BiasTest.DetectsCovering (1 ms) 25: [----------] 1 test from BiasTest (1 ms total) 25: 25: [----------] 1 test from gridTest 25: [ RUN ] gridTest.neighborhood 25: [ OK ] gridTest.neighborhood (3 ms) 25: [----------] 1 test from gridTest (3 ms total) 25: 25: [----------] 8 tests from WithParameters/BiasTest 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (19 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (6 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (2 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (9 ms) 25: [----------] 8 tests from WithParameters/BiasTest (43 ms total) 25: 25: [----------] 2 tests from WithParameters/BiasStateTest 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (8 ms) 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (8 ms) 25: [----------] 2 tests from WithParameters/BiasStateTest (16 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test cases ran. (64 ms total) 25: [ PASSED ] 12 tests. 25/27 Test #25: AwhTest .......................... Passed 0.67 sec test 26 Start 26: SimdUnitTests 26: Test command: /build/gromacs-2019.1/build/openmpi/bin/simd-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/SimdUnitTests.xml" 26: Test timeout computed to be: 30 26: [==========] Running 86 tests from 3 test cases. 26: [----------] Global test environment set-up. 26: [----------] 41 tests from SimdScalarTest 26: [ RUN ] SimdScalarTest.load 26: [ OK ] SimdScalarTest.load (0 ms) 26: [ RUN ] SimdScalarTest.loadU 26: [ OK ] SimdScalarTest.loadU (0 ms) 26: [ RUN ] SimdScalarTest.store 26: [ OK ] SimdScalarTest.store (0 ms) 26: [ RUN ] SimdScalarTest.storeU 26: [ OK ] SimdScalarTest.storeU (0 ms) 26: [ RUN ] SimdScalarTest.setZero 26: [ OK ] SimdScalarTest.setZero (0 ms) 26: [ RUN ] SimdScalarTest.andNot 26: [ OK ] SimdScalarTest.andNot (0 ms) 26: [ RUN ] SimdScalarTest.fma 26: [ OK ] SimdScalarTest.fma (0 ms) 26: [ RUN ] SimdScalarTest.fms 26: [ OK ] SimdScalarTest.fms (0 ms) 26: [ RUN ] SimdScalarTest.fnma 26: [ OK ] SimdScalarTest.fnma (0 ms) 26: [ RUN ] SimdScalarTest.fnms 26: [ OK ] SimdScalarTest.fnms (0 ms) 26: [ RUN ] SimdScalarTest.maskAdd 26: [ OK ] SimdScalarTest.maskAdd (0 ms) 26: [ RUN ] SimdScalarTest.maskzMul 26: [ OK ] SimdScalarTest.maskzMul (0 ms) 26: [ RUN ] SimdScalarTest.maskzFma 26: [ OK ] SimdScalarTest.maskzFma (0 ms) 26: [ RUN ] SimdScalarTest.abs 26: [ OK ] SimdScalarTest.abs (0 ms) 26: [ RUN ] SimdScalarTest.max 26: [ OK ] SimdScalarTest.max (0 ms) 26: [ RUN ] SimdScalarTest.min 26: [ OK ] SimdScalarTest.min (0 ms) 26: [ RUN ] SimdScalarTest.round 26: [ OK ] SimdScalarTest.round (0 ms) 26: [ RUN ] SimdScalarTest.trunc 26: [ OK ] SimdScalarTest.trunc (0 ms) 26: [ RUN ] SimdScalarTest.reduce 26: [ OK ] SimdScalarTest.reduce (0 ms) 26: [ RUN ] SimdScalarTest.testBits 26: [ OK ] SimdScalarTest.testBits (0 ms) 26: [ RUN ] SimdScalarTest.anyTrue 26: [ OK ] SimdScalarTest.anyTrue (0 ms) 26: [ RUN ] SimdScalarTest.selectByMask 26: [ OK ] SimdScalarTest.selectByMask (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMask 26: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 26: [ RUN ] SimdScalarTest.blend 26: [ OK ] SimdScalarTest.blend (0 ms) 26: [ RUN ] SimdScalarTest.cvtR2I 26: [ OK ] SimdScalarTest.cvtR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvttR2I 26: [ OK ] SimdScalarTest.cvttR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvtI2R 26: [ OK ] SimdScalarTest.cvtI2R (0 ms) 26: [ RUN ] SimdScalarTest.cvtF2D 26: [ OK ] SimdScalarTest.cvtF2D (0 ms) 26: [ RUN ] SimdScalarTest.cvtD2D 26: [ OK ] SimdScalarTest.cvtD2D (0 ms) 26: [ RUN ] SimdScalarTest.loadI 26: [ OK ] SimdScalarTest.loadI (0 ms) 26: [ RUN ] SimdScalarTest.loadUI 26: [ OK ] SimdScalarTest.loadUI (0 ms) 26: [ RUN ] SimdScalarTest.storeI 26: [ OK ] SimdScalarTest.storeI (0 ms) 26: [ RUN ] SimdScalarTest.storeUI 26: [ OK ] SimdScalarTest.storeUI (0 ms) 26: [ RUN ] SimdScalarTest.andNotI 26: [ OK ] SimdScalarTest.andNotI (0 ms) 26: [ RUN ] SimdScalarTest.testBitsI 26: [ OK ] SimdScalarTest.testBitsI (0 ms) 26: [ RUN ] SimdScalarTest.selectByMaskI 26: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMaskI 26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 26: [ RUN ] SimdScalarTest.blendI 26: [ OK ] SimdScalarTest.blendI (0 ms) 26: [ RUN ] SimdScalarTest.cvtB2IB 26: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 26: [ RUN ] SimdScalarTest.cvtIB2B 26: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 26: [ RUN ] SimdScalarTest.expandScalarsToTriplets 26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 26: [----------] 41 tests from SimdScalarTest (1 ms total) 26: 26: [----------] 8 tests from SimdScalarUtilTest 26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 26: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 26: 26: [----------] 37 tests from SimdScalarMathTest 26: [ RUN ] SimdScalarMathTest.copysign 26: [ OK ] SimdScalarMathTest.copysign (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPair 26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 26: [ RUN ] SimdScalarMathTest.inv 26: [ OK ] SimdScalarMathTest.inv (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrt 26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdScalarMathTest.log 26: [ OK ] SimdScalarMathTest.log (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2 26: [ OK ] SimdScalarMathTest.exp2 (0 ms) 26: [ RUN ] SimdScalarMathTest.exp 26: [ OK ] SimdScalarMathTest.exp (0 ms) 26: [ RUN ] SimdScalarMathTest.erf 26: [ OK ] SimdScalarMathTest.erf (0 ms) 26: [ RUN ] SimdScalarMathTest.erfc 26: [ OK ] SimdScalarMathTest.erfc (0 ms) 26: [ RUN ] SimdScalarMathTest.sincos 26: [ OK ] SimdScalarMathTest.sincos (0 ms) 26: [ RUN ] SimdScalarMathTest.sin 26: [ OK ] SimdScalarMathTest.sin (0 ms) 26: [ RUN ] SimdScalarMathTest.cos 26: [ OK ] SimdScalarMathTest.cos (0 ms) 26: [ RUN ] SimdScalarMathTest.tan 26: [ OK ] SimdScalarMathTest.tan (0 ms) 26: [ RUN ] SimdScalarMathTest.asin 26: [ OK ] SimdScalarMathTest.asin (0 ms) 26: [ RUN ] SimdScalarMathTest.acos 26: [ OK ] SimdScalarMathTest.acos (0 ms) 26: [ RUN ] SimdScalarMathTest.atan 26: [ OK ] SimdScalarMathTest.atan (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2 26: [ OK ] SimdScalarMathTest.atan2 (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrection 26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.invSingleAccuracy 26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.logSingleAccuracy 26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.expSingleAccuracy 26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 26: [----------] 37 tests from SimdScalarMathTest (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 86 tests from 3 test cases ran. (2 ms total) 26: [ PASSED ] 86 tests. 26/27 Test #26: SimdUnitTests .................... Passed 0.62 sec test 27 Start 27: CompatibilityHelpersTests 27: Test command: /build/gromacs-2019.1/build/openmpi/bin/compat-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/CompatibilityHelpersTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 6 tests from 6 test cases. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CompatibilityHelper 27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles 27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms) 27: [----------] 1 test from CompatibilityHelper (0 ms total) 27: 27: [----------] 1 test from NotNullConstruction 27: [ RUN ] NotNullConstruction.Works 27: [ OK ] NotNullConstruction.Works (0 ms) 27: [----------] 1 test from NotNullConstruction (0 ms total) 27: 27: [----------] 1 test from NotNullCasting 27: [ RUN ] NotNullCasting.Works 27: [ OK ] NotNullCasting.Works (0 ms) 27: [----------] 1 test from NotNullCasting (0 ms total) 27: 27: [----------] 1 test from NotNullAssignment 27: [ RUN ] NotNullAssignment.Works 27: [ OK ] NotNullAssignment.Works (0 ms) 27: [----------] 1 test from NotNullAssignment (0 ms total) 27: 27: [----------] 1 test from MakeNotNull 27: [ RUN ] MakeNotNull.Works 27: [ OK ] MakeNotNull.Works (0 ms) 27: [----------] 1 test from MakeNotNull (0 ms total) 27: 27: [----------] 1 test from NotNull 27: [ RUN ] NotNull.WorksInContainers 27: [ OK ] NotNull.WorksInContainers (0 ms) 27: [----------] 1 test from NotNull (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 6 tests from 6 test cases ran. (0 ms total) 27: [ PASSED ] 6 tests. 27/27 Test #27: CompatibilityHelpersTests ........ Passed 0.37 sec 100% tests passed, 0 tests failed out of 27 Label Time Summary: GTest = 23.02 sec*proc (27 tests) MpiTest = 3.03 sec*proc (3 tests) UnitTest = 23.02 sec*proc (27 tests) Total Test time (real) = 24.79 sec /usr/bin/make -j3 -C build/openmpi-dp tests make[1]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/openmpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/openmpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles 99 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 1%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend [ 3%] Built target tng_io_obj /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/external/googletest /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build [ 4%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target gmock make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build [ 22%] Built target libgromacs_generated make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googlemock/src/gmock-all.cc /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 22%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 23%] Built target mdrunutility-test-shared cd /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googletest/src/gtest-all.cc make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 80%] Built target libgromacs cd /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o /usr/bin/ranlib ../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 81%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/testutils /build/gromacs-2019.1/build/openmpi-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-2019.1/src/testutils/cmdlinetest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/gromacs-2019.1/src/testutils/conftest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/gromacs-2019.1/src/testutils/filematchers.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/interactivetest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/gromacs-2019.1/src/testutils/loggertest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpi-printer.cpp.o -c /build/gromacs-2019.1/src/testutils/mpi-printer.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/mpitest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata-xml.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata-xml.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/gromacs-2019.1/src/testutils/stdiohelper.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/gromacs-2019.1/src/testutils/stringtest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/gromacs-2019.1/src/testutils/testasserts.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/gromacs-2019.1/src/testutils/testfilemanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/gromacs-2019.1/src/testutils/testfileredirector.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/gromacs-2019.1/src/testutils/testinit.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/testmatchers.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/gromacs-2019.1/src/testutils/testoptions.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/textblockmatchers.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/gromacs-2019.1/src/testutils/xvgtest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/gromacs-2019.1/src/external/tinyxml2/tinyxml2.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi-printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata-xml.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 83%] Built target testutils /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/compat/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/make_unique.cpp Scanning dependencies of target testutils-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/mpitest.cpp Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/interactivetest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/refdata_tests.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 83%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 84%] Built target compat-test /usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdlib-test Scanning dependencies of target applied-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp:46: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/mdebin.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp:46: /usr/include/c++/8/bits/stl_vector.h: In function 'void {anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 84%] Built target applied-forces-test /usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color= Scanning dependencies of target listed-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/tests/bonded.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/settle.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/settle.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::SettleTest_SatisfiesConstraints_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/settle.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp:37: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 85%] Built target testutils-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/commandline/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/topology/block.h:42, from /build/gromacs-2019.1/src/gromacs/mdlib/shake.h:48, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector&, const std::vector&, const std::vector&, const std::vector&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/simulationsignal.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 85%] Built target listed-forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/domdec/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/hashedmap.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroups.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroups.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp:173:28: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 updateGroupsCog.addCogs(globalAtomIndices, positions); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp:173:28: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 85%] Built target domdec-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/ewald/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 86%] Built target mdlib-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fft/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineparser.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock.h:58, from /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 vector(initializer_list __l, ^~~~~~ make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 87%] Built target fft-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/gputest.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock.h:58, from /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock.h:58, from /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:97:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }; ^ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:165:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }; ^ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp:174:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }; ^ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/pargs.cpp In file included from /usr/include/c++/8/map:61, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock.h:58, from /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp:47: /usr/include/c++/8/bits/stl_map.h: In function 'std::map<_Key, _Tp, _Compare, _Alloc>::map(std::initializer_list >, const _Compare&, const allocator_type&) [with _Key = gmx::BasicVector; _Tp = t_complex; _Compare = std::less >; _Alloc = std::allocator, t_complex> >]': /usr/include/c++/8/bits/stl_map.h:226:7: note: parameter passing for argument of type 'std::initializer_list, t_complex> >' changed in GCC 7.1 map(initializer_list __l, ^~~ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp:343:1: note: parameter passing for argument of type 'std::initializer_list, t_complex> >' changed in GCC 7.1 }; ^ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp:343:1: note: parameter passing for argument of type 'std::initializer_list, t_complex> >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:43: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test::TestBody() [with gtest_TypeParam_ = double]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:57: /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void compareViews(ArrayRef input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void runTest(const gmx_gpu_info_t &gpuInfo, ^~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test::TestBody() [with gtest_TypeParam_ = double]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:57: /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef >, gmx::ArrayRef >) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void compareViews(ArrayRef < BasicVector < T>> input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef, gmx::ArrayRef) [with T = gmx::BasicVector]': /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void runTest(const gmx_gpu_info_t &gpuInfo, ^~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 88%] Built target commandline-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/hardware/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:43: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::HostAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/tests/hardwaretopology.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector, gmx::Allocator, gmx::HostAllocationPolicy> >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test::TestBody() [with gtest_TypeParam_ = gmx::BasicVector]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test::TestBody() [with gtest_TypeParam_ = gmx::BasicVector]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::HostAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46, from /build/gromacs-2019.1/src/external/googletest/googlemock/include/gmock/gmock.h:58, from /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; = void; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 vector(_InputIterator __first, _InputIterator __last, ^~~~~~ /usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:326:114: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 CoordinatesVector const c_sampleCoordinates1(c_sampleCoordinatesFull.begin(), c_sampleCoordinatesFull.begin() + 1); ^ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:328:118: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 CoordinatesVector const c_sampleCoordinates2(c_sampleCoordinatesFull.begin() + 1, c_sampleCoordinatesFull.begin() + 3); ^ /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:330:120: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 CoordinatesVector const c_sampleCoordinates13(c_sampleCoordinatesFull.begin() + 3, c_sampleCoordinatesFull.begin() + 16); ^ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 88%] Built target hardware-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/math/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmetestcommon.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 88%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/math/arrayrefwithpadding.h:49, from /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp:43: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/math/arrayrefwithpadding.h:49, from /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 89%] Built target ewald-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 89%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpmanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp:49: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 89%] Built target mdrunutility-mpi-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/options/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 90%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/random/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp In file included from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:59: /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef >, int) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void fillInputContents(ArrayRef < BasicVector < T>> inputRef, ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef, gmx::ArrayRef) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void compareViews(ArrayRef input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef >, gmx::ArrayRef >) [with T = double]': /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 void compareViews(ArrayRef < BasicVector < T>> input, ^~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef >' changed in GCC 7.1 cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoption.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = gmx::Allocator, gmx::AlignedAllocationPolicy>]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector, gmx::Allocator, gmx::AlignedAllocationPolicy> >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, gmx::Allocator, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoptionmanager.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector, std::allocator > >]': /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/seed.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/option.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp:50: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::RVecTest_ConvertsImplicitlyFrom_rvec_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm In file included from /usr/include/c++/8/vector:64, from /usr/include/c++/8/bits/random.h:34, from /usr/include/c++/8/random:49, from /build/gromacs-2019.1/src/gromacs/random/seed.h:51, from /build/gromacs-2019.1/src/gromacs/random/threefry.h:51, from /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:43: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 vector(initializer_list __l, ^~~~~~ make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 90%] Built target math-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/restraint/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/tests/manager.cpp /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)': /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 }}; ^ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformintdistribution.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 91%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tables/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/repeatingsection.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}}, ^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}}, ^~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]': /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}}, ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:56, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/external/googletest/googletest/include/gtest/gtest.h:58, from /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:50: /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~ /build/gromacs-2019.1/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_' GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_) ^~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX' EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}}, ^~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 92%] Built target random-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/timeunitmanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 92%] Built target table-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 93%] Built target taskassignment-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 94%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fileio/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp:48: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/filemd5.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 95%] Built target options-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/pulling/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 95%] Built target pull-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/awh/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm /usr/include/c++/8/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp:37: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 95%] Built target fileio-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/simd/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/base.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.h:57, from /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_math.cpp In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, double, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_memory.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 95%] Built target awh-test cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 97%] Built target simd-test cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask64.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask128.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/gmxregex.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/path.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [100%] Built target utility-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1 /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[1]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' (cd build/openmpi-dp ; LD_LIBRARY_PATH=/build/gromacs-2019.1/build/openmpi-dp/lib \ OMPI_MCA_plm_rsh_agent=/bin/false \ OMPI_MCA_rmaps_base_oversubscribe=1 \ ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 ) UpdateCTestConfiguration from :/build/gromacs-2019.1/build/openmpi-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/openmpi-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-2019.1/build/openmpi-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/openmpi-dp/DartConfiguration.tcl Test project /build/gromacs-2019.1/build/openmpi-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: TestUtilsUnitTests 1: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/testutils-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (40 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (83 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariants 1: [ OK ] ReferenceDataTest.HandlesVariants (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (14 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (1 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (0 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (0 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (1 ms) 1: [----------] 4 tests from XvgTests (3 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (101 ms total) 1: [ PASSED ] 59 tests. 1/27 Test #1: TestUtilsUnitTests ............... Passed 7.31 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /usr/bin/mpiexec.openmpi "-np" "2" "/build/gromacs-2019.1/build/openmpi-dp/bin/testutils-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (1 ms) 2: [----------] 1 test from MpiSelfTest (1 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (1 ms total) 2: [ PASSED ] 1 test. 2/27 Test #2: TestUtilsMpiUnitTests ............ Passed 0.71 sec test 3 Start 3: MdlibUnitTest 3: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/mdlib-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/MdlibUnitTest.xml" 3: Test timeout computed to be: 30 3: [==========] Running 50 tests from 8 test cases. 3: [----------] Global test environment set-up. 3: [----------] 1 test from VerletBufferConstraintTest 3: [ RUN ] VerletBufferConstraintTest.EqualMasses 3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 3: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 3: 3: [----------] 3 tests from PrintEbin 3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (141 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (104 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (13 ms) 3: [----------] 3 tests from PrintEbin (258 ms total) 3: 3: [----------] 4 tests from ShakeTest 3: [ RUN ] ShakeTest.ConstrainsOneBond 3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 3: [----------] 4 tests from ShakeTest (0 ms total) 3: 3: [----------] 1 test from NullSignalTest 3: [ RUN ] NullSignalTest.NullSignallerWorks 3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 3: [----------] 1 test from NullSignalTest (0 ms total) 3: 3: [----------] 7 tests from SignalTest 3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 3: [----------] 7 tests from SignalTest (0 ms total) 3: 3: [----------] 9 tests from UpdateGroups 3: [ RUN ] UpdateGroups.ethaneUA 3: [ OK ] UpdateGroups.ethaneUA (47 ms) 3: [ RUN ] UpdateGroups.methane 3: [ OK ] UpdateGroups.methane (0 ms) 3: [ RUN ] UpdateGroups.ethane 3: [ OK ] UpdateGroups.ethane (0 ms) 3: [ RUN ] UpdateGroups.butaneUA 3: [ OK ] UpdateGroups.butaneUA (0 ms) 3: [ RUN ] UpdateGroups.waterThreeSite 3: [ OK ] UpdateGroups.waterThreeSite (0 ms) 3: [ RUN ] UpdateGroups.waterFourSite 3: [ OK ] UpdateGroups.waterFourSite (0 ms) 3: [ RUN ] UpdateGroups.fourAtomsWithSettle 3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 3: [ RUN ] UpdateGroups.waterFlexAngle 3: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 3: [ RUN ] UpdateGroups.twoMoltypes 3: [ OK ] UpdateGroups.twoMoltypes (0 ms) 3: [----------] 9 tests from UpdateGroups (47 ms total) 3: 3: [----------] 1 test from UpdateGroupsCog 3: [ RUN ] UpdateGroupsCog.ComputesCogs 3: [ OK ] UpdateGroupsCog.ComputesCogs (25 ms) 3: [----------] 1 test from UpdateGroupsCog (25 ms total) 3: 3: [----------] 24 tests from WithParameters/SettleTest 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (1 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms) 3: [----------] 24 tests from WithParameters/SettleTest (2 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 50 tests from 8 test cases ran. (333 ms total) 3: [ PASSED ] 50 tests. 3/27 Test #3: MdlibUnitTest .................... Passed 1.25 sec test 4 Start 4: AppliedForcesUnitTest 4: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/applied-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 4: Test timeout computed to be: 30 4: [==========] Running 3 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 3 tests from ElectricFieldTest 4: [ RUN ] ElectricFieldTest.Static 4: [ OK ] ElectricFieldTest.Static (0 ms) 4: [ RUN ] ElectricFieldTest.Oscillating 4: [ OK ] ElectricFieldTest.Oscillating (0 ms) 4: [ RUN ] ElectricFieldTest.Pulsed 4: [ OK ] ElectricFieldTest.Pulsed (0 ms) 4: [----------] 3 tests from ElectricFieldTest (0 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 3 tests from 1 test case ran. (0 ms total) 4: [ PASSED ] 3 tests. 4/27 Test #4: AppliedForcesUnitTest ............ Passed 0.79 sec test 5 Start 5: ListedForcesTest 5: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/listed-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/ListedForcesTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 15 tests from 1 test case. 5: [----------] Global test environment set-up. 5: [----------] 15 tests from BondedTest 5: [ RUN ] BondedTest.BondAnglePbcNone 5: [ OK ] BondedTest.BondAnglePbcNone (71 ms) 5: [ RUN ] BondedTest.BondAnglePbcXy 5: [ OK ] BondedTest.BondAnglePbcXy (33 ms) 5: [ RUN ] BondedTest.BondAnglePbcXyz 5: [ OK ] BondedTest.BondAnglePbcXyz (34 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcNone 5: [ OK ] BondedTest.DihedralAnglePbcNone (16 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXy 5: [ OK ] BondedTest.DihedralAnglePbcXy (20 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXyz 5: [ OK ] BondedTest.DihedralAnglePbcXyz (1 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcNo 5: [ OK ] BondedTest.IfuncBondsPbcNo (24 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXy 5: [ OK ] BondedTest.IfuncBondsPbcXy (17 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXyz 5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcNo 5: [ OK ] BondedTest.IfuncAnglesPbcNo (21 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXy 5: [ OK ] BondedTest.IfuncAnglesPbcXy (16 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ 5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (58 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo 5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (13 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (37 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (1 ms) 5: [----------] 15 tests from BondedTest (363 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 15 tests from 1 test case ran. (363 ms total) 5: [ PASSED ] 15 tests. 5/27 Test #5: ListedForcesTest ................. Passed 1.47 sec test 6 Start 6: CommandLineUnitTests 6: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/commandline-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/CommandLineUnitTests.xml" 6: Test timeout computed to be: 30 6: [==========] Running 55 tests from 6 test cases. 6: [----------] Global test environment set-up. 6: [----------] 3 tests from CommandLineHelpModuleTest 6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (57 ms) 6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (49 ms) 6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (35 ms) 6: [----------] 3 tests from CommandLineHelpModuleTest (141 ms total) 6: 6: [----------] 6 tests from CommandLineHelpWriterTest 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (11 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (8 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (8 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms) 6: [----------] 6 tests from CommandLineHelpWriterTest (29 ms total) 6: 6: [----------] 6 tests from CommandLineModuleManagerTest 6: [ RUN ] CommandLineModuleManagerTest.RunsModule 6: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms) 6: [----------] 6 tests from CommandLineModuleManagerTest (2 ms total) 6: 6: [----------] 13 tests from CommandLineParserTest 6: [ RUN ] CommandLineParserTest.HandlesSingleValues 6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesString 6: [ OK ] CommandLineParserTest.HandlesString (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 6: [----------] 13 tests from CommandLineParserTest (1 ms total) 6: 6: [----------] 6 tests from CommandLineProgramContextTest 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (37 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 6: [----------] 6 tests from CommandLineProgramContextTest (37 ms total) 6: 6: [----------] 21 tests from ParseCommonArgsTest 6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (7 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (24 ms) 6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 6: [----------] 21 tests from ParseCommonArgsTest (33 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 55 tests from 6 test cases ran. (244 ms total) 6: [ PASSED ] 55 tests. 6/27 Test #6: CommandLineUnitTests ............. Passed 0.81 sec test 7 Start 7: DomDecTests 7: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/domdec-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/DomDecTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 9 tests from 2 test cases. 7: [----------] Global test environment set-up. 7: [----------] 7 tests from HashedMap 7: [ RUN ] HashedMap.InsertsFinds 7: [ OK ] HashedMap.InsertsFinds (0 ms) 7: [ RUN ] HashedMap.NegativeKeysWork 7: [ OK ] HashedMap.NegativeKeysWork (0 ms) 7: [ RUN ] HashedMap.InsertsErases 7: [ OK ] HashedMap.InsertsErases (0 ms) 7: [ RUN ] HashedMap.InsertsOrAssigns 7: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 7: [ RUN ] HashedMap.Clears 7: [ OK ] HashedMap.Clears (0 ms) 7: [ RUN ] HashedMap.LinkedEntries 7: [ OK ] HashedMap.LinkedEntries (0 ms) 7: [ RUN ] HashedMap.ResizesTable 7: [ OK ] HashedMap.ResizesTable (0 ms) 7: [----------] 7 tests from HashedMap (0 ms total) 7: 7: [----------] 2 tests from LocalAtomSetManager 7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 7: [----------] 2 tests from LocalAtomSetManager (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 9 tests from 2 test cases ran. (0 ms total) 7: [ PASSED ] 9 tests. 7/27 Test #7: DomDecTests ...................... Passed 0.50 sec test 8 Start 8: EwaldUnitTests 8: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/ewald-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/EwaldUnitTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 257 tests from 10 test cases. 8: [----------] Global test environment set-up. 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (215 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (215 ms total) 8: 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (117 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (82 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (27 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (56 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (53 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (34 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (29 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (57 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (34 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (36 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (16 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (56 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (49 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (32 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (41 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (35 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (26 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (40 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (16 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (28 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (43 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (34 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (22 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (24 ms) 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (992 ms total) 8: 8: [----------] 144 tests from SaneInput/PmeGatherTest 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (34 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (33 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (17 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (51 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (15 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (33 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (23 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (32 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (40 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (36 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (23 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (33 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (23 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (32 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (10 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (24 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (18 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (29 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (55 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (12 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (17 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (26 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (55 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (35 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (17 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (14 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (32 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (47 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (21 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (24 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (20 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (47 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (10 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (41 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (28 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (14 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (26 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (24 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (17 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (37 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (7 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (15 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (28 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (32 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (33 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (24 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (8 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (16 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (15 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (34 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (51 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (17 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (10 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (31 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (44 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (31 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (57 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (30 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (28 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (61 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (40 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (13 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (22 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (9 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (25 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms) 8: [----------] 144 tests from SaneInput/PmeGatherTest (2484 ms total) 8: 8: [----------] 16 tests from SaneInput/PmeSolveTest 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (4 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (21 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (29 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (15 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (8 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (15 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (24 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (17 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (35 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (26 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (15 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (11 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (14 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (9 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (19 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (14 ms) 8: [----------] 16 tests from SaneInput/PmeSolveTest (277 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (3 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (4 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (4 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (39 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (12 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (34 ms) 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (100 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (21 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (24 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (14 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (48 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (13 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (25 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (6 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (17 ms) 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (168 ms total) 8: 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (9 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (10 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (6 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (18 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (22 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (18 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (124 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (143 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (3 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (6 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (3 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (5 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (3 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (32 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (3 ms) 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (408 ms total) 8: 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (5 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (28 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (33 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (5 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (48 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (66 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (42 ms) 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (249 ms total) 8: 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (28 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (28 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (24 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (14 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (17 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (18 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (20 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (5 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (23 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (49 ms) 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (240 ms total) 8: 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (21 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (66 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (78 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (65 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (81 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (14 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (8 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (11 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (91 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (15 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (46 ms) 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (513 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 257 tests from 10 test cases ran. (5685 ms total) 8: [ PASSED ] 257 tests. 8/27 Test #8: EwaldUnitTests ................... Passed 6.48 sec test 9 Start 9: FFTUnitTests 9: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/fft-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/FFTUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 14 tests from 4 test cases. 9: [----------] Global test environment set-up. 9: [----------] 2 tests from ManyFFTTest 9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (18 ms) 9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (19 ms) 9: [----------] 2 tests from ManyFFTTest (38 ms total) 9: 9: [----------] 1 test from FFTTest 9: [ RUN ] FFTTest.Real2DLength18_15Test 9: [ OK ] FFTTest.Real2DLength18_15Test (8 ms) 9: [----------] 1 test from FFTTest (9 ms total) 9: 9: [----------] 1 test from FFFTest3D 9: [ RUN ] FFFTest3D.Real5_6_9 9: [ OK ] FFFTest3D.Real5_6_9 (5 ms) 9: [----------] 1 test from FFFTest3D (5 ms total) 9: 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (4 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (11 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (16 ms) 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (44 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 14 tests from 4 test cases ran. (96 ms total) 9: [ PASSED ] 14 tests. 9/27 Test #9: FFTUnitTests ..................... Passed 0.72 sec test 10 Start 10: GpuUtilsUnitTests 10: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 60 tests from 19 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/0 (1 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Swap 10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Comparison 10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Swap 10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Comparison 10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Swap 10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Comparison 10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Swap 10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Comparison 10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 10: 10: [----------] 1 test from HostAllocatorUntypedTest 10: [ RUN ] HostAllocatorUntypedTest.Comparison 10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.Move 10: [ OK ] AllocatorTest/0.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/0 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.Move 10: [ OK ] AllocatorTest/1.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/1 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.Move 10: [ OK ] AllocatorTest/2.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/2 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.Move 10: [ OK ] AllocatorTest/3.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/3 (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 60 tests from 19 test cases ran. (3 ms total) 10: [ PASSED ] 60 tests. 10/27 Test #10: GpuUtilsUnitTests ................ Passed 0.42 sec test 11 Start 11: HardwareUnitTests 11: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/hardware-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/HardwareUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 4 tests from 1 test case. 11: [----------] Global test environment set-up. 11: [----------] 4 tests from HardwareTopologyTest 11: [ RUN ] HardwareTopologyTest.Execute 11: [ OK ] HardwareTopologyTest.Execute (14 ms) 11: [ RUN ] HardwareTopologyTest.HwlocExecute 11: [ OK ] HardwareTopologyTest.HwlocExecute (13 ms) 11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (13 ms) 11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (13 ms) 11: [----------] 4 tests from HardwareTopologyTest (53 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 4 tests from 1 test case ran. (53 ms total) 11: [ PASSED ] 4 tests. 11/27 Test #11: HardwareUnitTests ................ Passed 0.52 sec test 12 Start 12: MathUnitTests 12: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/math-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/MathUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 112 tests from 20 test cases. 12: [----------] Global test environment set-up. 12: [----------] 1 test from EmptyArrayRefWithPaddingTest 12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 12: 12: [----------] 6 tests from StructureSimilarityTest 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 12: [----------] 6 tests from StructureSimilarityTest (0 ms total) 12: 12: [----------] 21 tests from FunctionTest 12: [ RUN ] FunctionTest.StaticLog2 12: [ OK ] FunctionTest.StaticLog2 (61 ms) 12: [ RUN ] FunctionTest.Log2I32Bit 12: [ OK ] FunctionTest.Log2I32Bit (17 ms) 12: [ RUN ] FunctionTest.Log2I64Bit 12: [ OK ] FunctionTest.Log2I64Bit (17 ms) 12: [ RUN ] FunctionTest.GreatestCommonDivisor 12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 12: [ RUN ] FunctionTest.InvsqrtFloat 12: [ OK ] FunctionTest.InvsqrtFloat (16 ms) 12: [ RUN ] FunctionTest.InvsqrtDouble 12: [ OK ] FunctionTest.InvsqrtDouble (16 ms) 12: [ RUN ] FunctionTest.InvsqrtInteger 12: [ OK ] FunctionTest.InvsqrtInteger (17 ms) 12: [ RUN ] FunctionTest.InvcbrtFloat 12: [ OK ] FunctionTest.InvcbrtFloat (17 ms) 12: [ RUN ] FunctionTest.InvcbrtDouble 12: [ OK ] FunctionTest.InvcbrtDouble (25 ms) 12: [ RUN ] FunctionTest.InvcbrtInteger 12: [ OK ] FunctionTest.InvcbrtInteger (25 ms) 12: [ RUN ] FunctionTest.SixthrootFloat 12: [ OK ] FunctionTest.SixthrootFloat (1 ms) 12: [ RUN ] FunctionTest.SixthrootDouble 12: [ OK ] FunctionTest.SixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.SixthrootInteger 12: [ OK ] FunctionTest.SixthrootInteger (24 ms) 12: [ RUN ] FunctionTest.InvsixthrootFloat 12: [ OK ] FunctionTest.InvsixthrootFloat (25 ms) 12: [ RUN ] FunctionTest.InvsixthrootDouble 12: [ OK ] FunctionTest.InvsixthrootDouble (25 ms) 12: [ RUN ] FunctionTest.InvsixthrootInteger 12: [ OK ] FunctionTest.InvsixthrootInteger (25 ms) 12: [ RUN ] FunctionTest.Powers 12: [ OK ] FunctionTest.Powers (0 ms) 12: [ RUN ] FunctionTest.ErfInvFloat 12: [ OK ] FunctionTest.ErfInvFloat (25 ms) 12: [ RUN ] FunctionTest.ErfInvDouble 12: [ OK ] FunctionTest.ErfInvDouble (1 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms) 12: [----------] 21 tests from FunctionTest (338 ms total) 12: 12: [----------] 2 tests from InvertMatrixTest 12: [ RUN ] InvertMatrixTest.IdentityIsImpotent 12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertMatrixTest.ComputesInverse 12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 12: [----------] 2 tests from InvertMatrixTest (0 ms total) 12: 12: [----------] 2 tests from InvertBoxMatrixTest 12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanCopyAssign 12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanMoveAssign 12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanSwap 12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanCopyAssign 12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanMoveAssign 12: [ OK ] PaddedVectorTest/1.CanMoveAssign (1 ms) 12: [ RUN ] PaddedVectorTest/1.CanSwap 12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/1 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanCopyAssign 12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanMoveAssign 12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanSwap 12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanCopyAssign 12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanMoveAssign 12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanSwap 12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanCopyAssign 12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanMoveAssign 12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanSwap 12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanCopyAssign 12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanMoveAssign 12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanSwap 12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanCopyAssign 12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanMoveAssign 12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanSwap 12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanCopyAssign 12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanMoveAssign 12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanSwap 12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanCopyAssign 12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanMoveAssign 12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanSwap 12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/8 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanCopyAssign 12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanMoveAssign 12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanSwap 12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 12: 12: [----------] 33 tests from RVecTest 12: [ RUN ] RVecTest.CanBeStoredInVector 12: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAsMutable_rvec 12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Array 12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 12: [ RUN ] RVecTest.CanAddRVecToRvec 12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanAddAssignRVecToRvec 12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractRVecFromRvec 12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanDotProductRVecByRvec 12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanCrossProductRVecByRvec 12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVecInplace 12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 12: [ RUN ] RVecTest.CanScaleRVec 12: [ OK ] RVecTest.CanScaleRVec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVec 12: [ OK ] RVecTest.CanDivideRVec (0 ms) 12: [ RUN ] RVecTest.CanDoUnitvFromRVec 12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanSqLengthOfRVec 12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanLengthOfRVec 12: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToRVec 12: [ OK ] RVecTest.CanCastToRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToDVec 12: [ OK ] RVecTest.CanCastToDVec (0 ms) 12: [ RUN ] RVecTest.CanLeftScalarMultiply 12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanRightScalarMultiply 12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanGetUnitvFromRVec 12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanGetSqLengthOfRVec 12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanGetLengthOfRVec 12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoCrossProductOfRVec 12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoDotProductOfRVec 12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 12: [ RUN ] RVecTest.WorksAs_dvec_Reference 12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_ivec_Reference 12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Reference 12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 12: [ RUN ] RVecTest.CopyConstructorWorks 12: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 12: [ RUN ] RVecTest.CopyAssignmentWorks 12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 12: [ RUN ] RVecTest.MoveConstructorWorks 12: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 12: [ RUN ] RVecTest.MoveAssignmentWorks 12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 12: [----------] 33 tests from RVecTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 112 tests from 20 test cases ran. (341 ms total) 12: [ PASSED ] 112 tests. 12/27 Test #12: MathUnitTests .................... Passed 0.81 sec test 13 Start 13: MdrunUtilityUnitTests 13: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 17 tests from 1 test case. 13: [----------] Global test environment set-up. 13: [----------] 17 tests from ThreadAffinityTest 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 13: NOTE: Affinity setting failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 13: NOTE: Affinity setting for 1/2 threads failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms) 13: [----------] 17 tests from ThreadAffinityTest (9 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 17 tests from 1 test case ran. (9 ms total) 13: [ PASSED ] 17 tests. 13/27 Test #13: MdrunUtilityUnitTests ............ Passed 0.48 sec test 14 Start 14: MdrunUtilityMpiUnitTests 14: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "/build/gromacs-2019.1/build/openmpi-dp/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 13 tests from 2 test cases. 14: [----------] Global test environment set-up. 14: [----------] 6 tests from ThreadAffinityMultiRankTest 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (47 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (52 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (51 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (39 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (36 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (35 ms) 14: [----------] 6 tests from ThreadAffinityMultiRankTest (299 ms total) 14: 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (30 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (52 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (63 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (36 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (27 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (27 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (27 ms) 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (323 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 13 tests from 2 test cases ran. (626 ms total) 14: [ PASSED ] 13 tests. 14/27 Test #14: MdrunUtilityMpiUnitTests ......... Passed 1.20 sec test 15 Start 15: OnlineHelpUnitTests 15: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 22 tests from 4 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from TextTableFormatterTest 15: [ RUN ] TextTableFormatterTest.HandlesBasicCase 15: [ OK ] TextTableFormatterTest.HandlesBasicCase (23 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (25 ms) 15: [ RUN ] TextTableFormatterTest.HandlesIndentation 15: [ OK ] TextTableFormatterTest.HandlesIndentation (25 ms) 15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (25 ms) 15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (17 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (16 ms) 15: [----------] 6 tests from TextTableFormatterTest (131 ms total) 15: 15: [----------] 3 tests from HelpManagerTest 15: [ RUN ] HelpManagerTest.HandlesRootTopic 15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 15: [ RUN ] HelpManagerTest.HandlesSubTopics 15: [ OK ] HelpManagerTest.HandlesSubTopics (1 ms) 15: [ RUN ] HelpManagerTest.HandlesInvalidTopics 15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 15: [----------] 3 tests from HelpManagerTest (1 ms total) 15: 15: [----------] 2 tests from HelpTopicFormattingTest 15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (24 ms) 15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (17 ms) 15: [----------] 2 tests from HelpTopicFormattingTest (41 ms total) 15: 15: [----------] 11 tests from HelpWriterContextTest 15: [ RUN ] HelpWriterContextTest.FormatsParagraphs 15: [ OK ] HelpWriterContextTest.FormatsParagraphs (25 ms) 15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (17 ms) 15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (25 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralText 15: [ OK ] HelpWriterContextTest.FormatsLiteralText (25 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (25 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (25 ms) 15: [ RUN ] HelpWriterContextTest.FormatsBulletList 15: [ OK ] HelpWriterContextTest.FormatsBulletList (16 ms) 15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (17 ms) 15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (200 ms) 15: [ RUN ] HelpWriterContextTest.FormatsGridTable 15: [ OK ] HelpWriterContextTest.FormatsGridTable (59 ms) 15: [ RUN ] HelpWriterContextTest.FormatsTitles 15: [ OK ] HelpWriterContextTest.FormatsTitles (133 ms) 15: [----------] 11 tests from HelpWriterContextTest (567 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 22 tests from 4 test cases ran. (740 ms total) 15: [ PASSED ] 22 tests. 15/27 Test #15: OnlineHelpUnitTests .............. Passed 1.14 sec test 16 Start 16: OptionsUnitTests 16: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/options-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/OptionsUnitTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 110 tests from 18 test cases. 16: [----------] Global test environment set-up. 16: [----------] 5 tests from AbstractOptionStorageTest 16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 16: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 16: 16: [----------] 8 tests from FileNameOptionTest 16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 16: [----------] 8 tests from FileNameOptionTest (0 ms total) 16: 16: [----------] 15 tests from FileNameOptionManagerTest 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 16: 16: [----------] 1 test from OptionsTest 16: [ RUN ] OptionsTest.FailsOnNonsafeStorage 16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 16: [----------] 1 test from OptionsTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerTest 16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMissingValue 16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesExtraValue 16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesGroups 16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesSections 16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 16: [----------] 9 tests from OptionsAssignerTest (0 ms total) 16: 16: [----------] 4 tests from OptionsAssignerBooleanTest 16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 16: 16: [----------] 13 tests from OptionsAssignerIntegerTest 16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (1 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 16: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total) 16: 16: [----------] 5 tests from OptionsAssignerDoubleTest 16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 16: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerStringTest 16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 16: 16: [----------] 6 tests from OptionsAssignerEnumTest 16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total) 16: 16: [----------] 8 tests from RepeatingOptionSectionTest 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 16: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 16: 16: [----------] 1 test from TimeUnitManagerTest 16: [ RUN ] TimeUnitManagerTest.BasicOperations 16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 16: [----------] 1 test from TimeUnitManagerTest (0 ms total) 16: 16: [----------] 4 tests from TimeUnitBehaviorTest 16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 16: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 16: 16: [----------] 2 tests from TreeValueSupportAssignTest 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (22 ms) 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 16: [----------] 2 tests from TreeValueSupportAssignTest (22 ms total) 16: 16: [----------] 1 test from TreeValueSupportAssignErrorTest 16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 16: 16: [----------] 5 tests from TreeValueSupportCheckTest 16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 16: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 16: 16: [----------] 6 tests from TreeValueSupportAdjustTest 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (27 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (33 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (33 ms) 16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (34 ms) 16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (41 ms) 16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (25 ms) 16: [----------] 6 tests from TreeValueSupportAdjustTest (193 ms total) 16: 16: [----------] 8 tests from TreeValueSupportTest 16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (17 ms) 16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (16 ms) 16: [ RUN ] TreeValueSupportTest.SupportsInt64Option 16: [ OK ] TreeValueSupportTest.SupportsInt64Option (17 ms) 16: [ RUN ] TreeValueSupportTest.SupportsStringOption 16: [ OK ] TreeValueSupportTest.SupportsStringOption (17 ms) 16: [ RUN ] TreeValueSupportTest.SupportsFloatOption 16: [ OK ] TreeValueSupportTest.SupportsFloatOption (25 ms) 16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (25 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (25 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumOption 16: [ OK ] TreeValueSupportTest.SupportsEnumOption (33 ms) 16: [----------] 8 tests from TreeValueSupportTest (175 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 110 tests from 18 test cases ran. (395 ms total) 16: [ PASSED ] 110 tests. 16/27 Test #16: OptionsUnitTests ................. Passed 0.73 sec test 17 Start 17: RandomUnitTests 17: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/random-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/RandomUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 44 tests from 10 test cases. 17: [----------] Global test environment set-up. 17: [----------] 4 tests from ExponentialDistributionTest 17: [ RUN ] ExponentialDistributionTest.Output 17: [ OK ] ExponentialDistributionTest.Output (366 ms) 17: [ RUN ] ExponentialDistributionTest.Logical 17: [ OK ] ExponentialDistributionTest.Logical (0 ms) 17: [ RUN ] ExponentialDistributionTest.Reset 17: [ OK ] ExponentialDistributionTest.Reset (0 ms) 17: [ RUN ] ExponentialDistributionTest.AltParam 17: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from ExponentialDistributionTest (366 ms total) 17: 17: [----------] 4 tests from GammaDistributionTest 17: [ RUN ] GammaDistributionTest.Output 17: [ OK ] GammaDistributionTest.Output (25 ms) 17: [ RUN ] GammaDistributionTest.Logical 17: [ OK ] GammaDistributionTest.Logical (0 ms) 17: [ RUN ] GammaDistributionTest.Reset 17: [ OK ] GammaDistributionTest.Reset (0 ms) 17: [ RUN ] GammaDistributionTest.AltParam 17: [ OK ] GammaDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from GammaDistributionTest (25 ms total) 17: 17: [----------] 4 tests from NormalDistributionTest 17: [ RUN ] NormalDistributionTest.Output 17: [ OK ] NormalDistributionTest.Output (32 ms) 17: [ RUN ] NormalDistributionTest.Logical 17: [ OK ] NormalDistributionTest.Logical (0 ms) 17: [ RUN ] NormalDistributionTest.Reset 17: [ OK ] NormalDistributionTest.Reset (0 ms) 17: [ RUN ] NormalDistributionTest.AltParam 17: [ OK ] NormalDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from NormalDistributionTest (32 ms total) 17: 17: [----------] 1 test from SeedTest 17: [ RUN ] SeedTest.makeRandomSeed 17: [ OK ] SeedTest.makeRandomSeed (0 ms) 17: [----------] 1 test from SeedTest (0 ms total) 17: 17: [----------] 6 tests from TabulatedNormalDistributionTest 17: [ RUN ] TabulatedNormalDistributionTest.Output14 17: [ OK ] TabulatedNormalDistributionTest.Output14 (42 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Output16 17: [ OK ] TabulatedNormalDistributionTest.Output16 (34 ms) 17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (41 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Logical 17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Reset 17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.AltParam 17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 17: [----------] 6 tests from TabulatedNormalDistributionTest (117 ms total) 17: 17: [----------] 1 test from TabulatedNormalDistributionTableTest 17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (5 ms) 17: [----------] 1 test from TabulatedNormalDistributionTableTest (5 ms total) 17: 17: [----------] 6 tests from ThreeFry2x64Test 17: [ RUN ] ThreeFry2x64Test.Logical 17: [ OK ] ThreeFry2x64Test.Logical (0 ms) 17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (20 ms) 17: [ RUN ] ThreeFry2x64Test.Reseed 17: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 17: [ RUN ] ThreeFry2x64Test.Discard 17: [ OK ] ThreeFry2x64Test.Discard (0 ms) 17: [ RUN ] ThreeFry2x64Test.InvalidCounter 17: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 17: [----------] 6 tests from ThreeFry2x64Test (20 ms total) 17: 17: [----------] 4 tests from UniformIntDistributionTest 17: [ RUN ] UniformIntDistributionTest.Output 17: [ OK ] UniformIntDistributionTest.Output (33 ms) 17: [ RUN ] UniformIntDistributionTest.Logical 17: [ OK ] UniformIntDistributionTest.Logical (0 ms) 17: [ RUN ] UniformIntDistributionTest.Reset 17: [ OK ] UniformIntDistributionTest.Reset (0 ms) 17: [ RUN ] UniformIntDistributionTest.AltParam 17: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from UniformIntDistributionTest (33 ms total) 17: 17: [----------] 5 tests from UniformRealDistributionTest 17: [ RUN ] UniformRealDistributionTest.GenerateCanonical 17: [ OK ] UniformRealDistributionTest.GenerateCanonical (33 ms) 17: [ RUN ] UniformRealDistributionTest.Output 17: [ OK ] UniformRealDistributionTest.Output (108 ms) 17: [ RUN ] UniformRealDistributionTest.Logical 17: [ OK ] UniformRealDistributionTest.Logical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Reset 17: [ OK ] UniformRealDistributionTest.Reset (0 ms) 17: [ RUN ] UniformRealDistributionTest.AltParam 17: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 17: [----------] 5 tests from UniformRealDistributionTest (141 ms total) 17: 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (33 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (26 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (24 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (25 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (24 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (25 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (24 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (9 ms) 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (192 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 44 tests from 10 test cases ran. (933 ms total) 17: [ PASSED ] 44 tests. 17/27 Test #17: RandomUnitTests .................. Passed 2.76 sec test 18 Start 18: RestraintTests 18: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/RestraintTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 1 test from 1 test case. 18: [----------] Global test environment set-up. 18: [----------] 1 test from RestraintManager 18: [ RUN ] RestraintManager.restraintList 18: [ OK ] RestraintManager.restraintList (0 ms) 18: [----------] 1 test from RestraintManager (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1 test from 1 test case ran. (0 ms total) 18: [ PASSED ] 1 test. 18/27 Test #18: RestraintTests ................... Passed 0.36 sec test 19 Start 19: TableUnitTests 19: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/table-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/TableUnitTests.xml" 19: Test timeout computed to be: 30 19: [==========] Running 16 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (5 ms) 19: [ RUN ] SplineTableTest/0.Sinc 19: [ OK ] SplineTableTest/0.Sinc (2 ms) 19: [ RUN ] SplineTableTest/0.LJ12 19: [ OK ] SplineTableTest/0.LJ12 (65 ms) 19: [ RUN ] SplineTableTest/0.PmeCorrection 19: [ OK ] SplineTableTest/0.PmeCorrection (4 ms) 19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (4 ms) 19: [ RUN ] SplineTableTest/0.TwoFunctions 19: [ OK ] SplineTableTest/0.TwoFunctions (130 ms) 19: [ RUN ] SplineTableTest/0.ThreeFunctions 19: [ OK ] SplineTableTest/0.ThreeFunctions (146 ms) 19: [----------] 8 tests from SplineTableTest/0 (358 ms total) 19: 19: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (5 ms) 19: [ RUN ] SplineTableTest/1.Sinc 19: [ OK ] SplineTableTest/1.Sinc (5 ms) 19: [ RUN ] SplineTableTest/1.LJ12 19: [ OK ] SplineTableTest/1.LJ12 (164 ms) 19: [ RUN ] SplineTableTest/1.PmeCorrection 19: [ OK ] SplineTableTest/1.PmeCorrection (5 ms) 19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (3 ms) 19: [ RUN ] SplineTableTest/1.TwoFunctions 19: [ OK ] SplineTableTest/1.TwoFunctions (335 ms) 19: [ RUN ] SplineTableTest/1.ThreeFunctions 19: [ OK ] SplineTableTest/1.ThreeFunctions (374 ms) 19: [----------] 8 tests from SplineTableTest/1 (892 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 16 tests from 2 test cases ran. (1250 ms total) 19: [ PASSED ] 16 tests. 19/27 Test #19: TableUnitTests ................... Passed 1.73 sec test 20 Start 20: TaskAssignmentUnitTests 20: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 3 tests from 1 test case. 20: [----------] Global test environment set-up. 20: [----------] 3 tests from GpuIdStringHandlingTest 20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork 20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid 20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow 20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (0 ms) 20: [----------] 3 tests from GpuIdStringHandlingTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 3 tests from 1 test case ran. (0 ms total) 20: [ PASSED ] 3 tests. 20/27 Test #20: TaskAssignmentUnitTests .......... Passed 0.60 sec test 21 Start 21: UtilityUnitTests 21: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/utility-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/UtilityUnitTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 325 tests from 52 test cases. 21: [----------] Global test environment set-up. 21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.Move 21: [ OK ] AllocatorTest/0.Move (0 ms) 21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/0 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.Move 21: [ OK ] AllocatorTest/1.Move (0 ms) 21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/1 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.Move 21: [ OK ] AllocatorTest/2.Move (0 ms) 21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/2 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.Move 21: [ OK ] AllocatorTest/3.Move (0 ms) 21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/3 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.Move 21: [ OK ] AllocatorTest/4.Move (0 ms) 21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/4 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/5.Move 21: [ OK ] AllocatorTest/5.Move (0 ms) 21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/5 (1 ms total) 21: 21: [----------] 1 test from AllocatorUntypedTest 21: [ RUN ] AllocatorUntypedTest.Comparison 21: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 21: [----------] 1 test from AllocatorUntypedTest (0 ms total) 21: 21: [----------] 1 test from EmptyArrayRefTest 21: [ RUN ] EmptyArrayRefTest.IsEmpty 21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyArrayRefTest (0 ms total) 21: 21: [----------] 1 test from EmptyConstArrayRefTest 21: [ RUN ] EmptyConstArrayRefTest.IsEmpty 21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/3 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/13 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (1 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/16 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 21: 21: [----------] 4 tests from KeyValueTreeSerializerTest 21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (45 ms) 21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (25 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (24 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (17 ms) 21: [----------] 4 tests from KeyValueTreeSerializerTest (111 ms total) 21: 21: [----------] 6 tests from TreeValueTransformTest 21: [ RUN ] TreeValueTransformTest.SimpleTransforms 21: [ OK ] TreeValueTransformTest.SimpleTransforms (25 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromString 21: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 21: [ RUN ] TreeValueTransformTest.ScopedTransformRules 21: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 21: [----------] 6 tests from TreeValueTransformTest (27 ms total) 21: 21: [----------] 1 test from TreeValueTransformErrorTest 21: [ RUN ] TreeValueTransformErrorTest.ConversionError 21: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 21: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 21: 21: [----------] 2 tests from RegexBasicTest 21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported 21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (0 ms) 21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported 21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (1 ms) 21: [----------] 2 tests from RegexBasicTest (1 ms total) 21: 21: [----------] 5 tests from LoggerTest 21: [ RUN ] LoggerTest.EmptyLoggerWorks 21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToStream 21: [ OK ] LoggerTest.LogsToStream (1 ms) 21: [ RUN ] LoggerTest.LogsToFile 21: [ OK ] LoggerTest.LogsToFile (21 ms) 21: [ RUN ] LoggerTest.LevelFilteringWorks 21: [ OK ] LoggerTest.LevelFilteringWorks (15 ms) 21: [ RUN ] LoggerTest.LogsToMultipleStreams 21: [ OK ] LoggerTest.LogsToMultipleStreams (26 ms) 21: [----------] 5 tests from LoggerTest (64 ms total) 21: 21: [----------] 4 tests from MutexBasicTest 21: [ RUN ] MutexBasicTest.CanBeMade 21: [ OK ] MutexBasicTest.CanBeMade (0 ms) 21: [ RUN ] MutexBasicTest.CanBeLocked 21: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeTryLocked 21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 21: [----------] 4 tests from MutexBasicTest (0 ms total) 21: 21: [----------] 3 tests from MutexTaskTest 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (1 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 21: [----------] 3 tests from MutexTaskTest (1 ms total) 21: 21: [----------] 4 tests from PathTest 21: [ RUN ] PathTest.StripSourcePrefixWorks 21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks 21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathWorks 21: [ OK ] PathTest.GetParentPathWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathAndBasenameWorks 21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms) 21: [----------] 4 tests from PathTest (0 ms total) 21: 21: [----------] 2 tests from PhysicalNodeCommunicatorTest 21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 21: 21: [----------] 7 tests from StringUtilityTest 21: [ RUN ] StringUtilityTest.StartsWith 21: [ OK ] StringUtilityTest.StartsWith (0 ms) 21: [ RUN ] StringUtilityTest.EndsWith 21: [ OK ] StringUtilityTest.EndsWith (0 ms) 21: [ RUN ] StringUtilityTest.StripSuffixIfPresent 21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 21: [ RUN ] StringUtilityTest.StripString 21: [ OK ] StringUtilityTest.StripString (0 ms) 21: [ RUN ] StringUtilityTest.SplitString 21: [ OK ] StringUtilityTest.SplitString (0 ms) 21: [ RUN ] StringUtilityTest.SplitDelimitedString 21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms) 21: [----------] 7 tests from StringUtilityTest (1 ms total) 21: 21: [----------] 2 tests from FormatStringTest 21: [ RUN ] FormatStringTest.HandlesBasicFormatting 21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 21: [ RUN ] FormatStringTest.HandlesLongStrings 21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 21: [----------] 2 tests from FormatStringTest (0 ms total) 21: 21: [----------] 1 test from StringFormatterTest 21: [ RUN ] StringFormatterTest.HandlesBasicFormatting 21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 21: [----------] 1 test from StringFormatterTest (0 ms total) 21: 21: [----------] 1 test from formatAndJoinTest 21: [ RUN ] formatAndJoinTest.Works 21: [ OK ] formatAndJoinTest.Works (0 ms) 21: [----------] 1 test from formatAndJoinTest (0 ms total) 21: 21: [----------] 1 test from JoinStringsTest 21: [ RUN ] JoinStringsTest.Works 21: [ OK ] JoinStringsTest.Works (0 ms) 21: [----------] 1 test from JoinStringsTest (0 ms total) 21: 21: [----------] 6 tests from ReplaceAllTest 21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesNoMatches 21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 21: [----------] 6 tests from ReplaceAllTest (0 ms total) 21: 21: [----------] 10 tests from TextLineWrapperTest 21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (1 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectly 21: [ OK ] TextLineWrapperTest.WrapsCorrectly (54 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (50 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndent 21: [ OK ] TextLineWrapperTest.HandlesIndent (33 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (23 ms) 21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (19 ms) 21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (25 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (15 ms) 21: [----------] 10 tests from TextLineWrapperTest (220 ms total) 21: 21: [----------] 6 tests from TextWriterTest 21: [ RUN ] TextWriterTest.WritesLines 21: [ OK ] TextWriterTest.WritesLines (9 ms) 21: [ RUN ] TextWriterTest.WritesLinesInParts 21: [ OK ] TextWriterTest.WritesLinesInParts (16 ms) 21: [ RUN ] TextWriterTest.WritesWrappedLines 21: [ OK ] TextWriterTest.WritesWrappedLines (18 ms) 21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (50 ms) 21: [ RUN ] TextWriterTest.TracksNewlines 21: [ OK ] TextWriterTest.TracksNewlines (33 ms) 21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (90 ms) 21: [----------] 6 tests from TextWriterTest (217 ms total) 21: 21: [----------] 1 test from TypeTraitsTest 21: [ RUN ] TypeTraitsTest.IsIntegralConstant 21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 21: [----------] 1 test from TypeTraitsTest (0 ms total) 21: 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (1 ms) 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (1 ms total) 21: 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 21: 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total) 21: 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (1 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 325 tests from 52 test cases ran. (654 ms total) 21: [ PASSED ] 325 tests. 21/27 Test #21: UtilityUnitTests ................. Passed 0.91 sec test 22 Start 22: UtilityMpiUnitTests 22: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "/build/gromacs-2019.1/build/openmpi-dp/bin/utility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 2 tests from 1 test case. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from PhysicalNodeCommunicatorTest 22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (82 ms) 22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (31 ms) 22: [----------] 2 tests from PhysicalNodeCommunicatorTest (126 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test case ran. (128 ms total) 22: [ PASSED ] 2 tests. 22/27 Test #22: UtilityMpiUnitTests .............. Passed 0.60 sec test 23 Start 23: FileIOTests 23: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/fileio-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/FileIOTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 17 tests from 4 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from FileMD5Test 23: [ RUN ] FileMD5Test.CanComputeMD5 23: [ OK ] FileMD5Test.CanComputeMD5 (52 ms) 23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 23: [----------] 2 tests from FileMD5Test (52 ms total) 23: 23: [----------] 9 tests from ReadTest 23: [ RUN ] ReadTest.get_eint_ReadsInteger 23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_eint64_ReadsInteger 23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (1 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsInteger 23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsFloat 23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 23: [ RUN ] ReadTest.get_ereal_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not a 23: real value 23: 23: 23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 23: [----------] 9 tests from ReadTest (1 ms total) 23: 23: [----------] 2 tests from TngTest 23: [ RUN ] TngTest.CanOpenTngFile 23: [ OK ] TngTest.CanOpenTngFile (93 ms) 23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 23: [----------] 2 tests from TngTest (93 ms total) 23: 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (33 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (95 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (130 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 17 tests from 4 test cases ran. (276 ms total) 23: [ PASSED ] 17 tests. 23/27 Test #23: FileIOTests ...................... Passed 1.08 sec test 24 Start 24: PullTest 24: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/pull-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/PullTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 5 tests from 1 test case. 24: [----------] Global test environment set-up. 24: [----------] 5 tests from PullTest 24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 24: [----------] 5 tests from PullTest (1 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 5 tests from 1 test case ran. (1 ms total) 24: [ PASSED ] 5 tests. 24/27 Test #24: PullTest ......................... Passed 0.50 sec test 25 Start 25: AwhTest 25: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/awh-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/AwhTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 12 tests from 4 test cases. 25: [----------] Global test environment set-up. 25: [----------] 1 test from BiasTest 25: [ RUN ] BiasTest.DetectsCovering 25: [ OK ] BiasTest.DetectsCovering (3 ms) 25: [----------] 1 test from BiasTest (3 ms total) 25: 25: [----------] 1 test from gridTest 25: [ RUN ] gridTest.neighborhood 25: [ OK ] gridTest.neighborhood (4 ms) 25: [----------] 1 test from gridTest (4 ms total) 25: 25: [----------] 8 tests from WithParameters/BiasTest 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (47 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (2 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (2 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (2 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (2 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (2 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms) 25: [----------] 8 tests from WithParameters/BiasTest (60 ms total) 25: 25: [----------] 2 tests from WithParameters/BiasStateTest 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (2 ms) 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (5 ms) 25: [----------] 2 tests from WithParameters/BiasStateTest (7 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test cases ran. (74 ms total) 25: [ PASSED ] 12 tests. 25/27 Test #25: AwhTest .......................... Passed 0.49 sec test 26 Start 26: SimdUnitTests 26: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/simd-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/SimdUnitTests.xml" 26: Test timeout computed to be: 30 26: [==========] Running 86 tests from 3 test cases. 26: [----------] Global test environment set-up. 26: [----------] 41 tests from SimdScalarTest 26: [ RUN ] SimdScalarTest.load 26: [ OK ] SimdScalarTest.load (0 ms) 26: [ RUN ] SimdScalarTest.loadU 26: [ OK ] SimdScalarTest.loadU (0 ms) 26: [ RUN ] SimdScalarTest.store 26: [ OK ] SimdScalarTest.store (0 ms) 26: [ RUN ] SimdScalarTest.storeU 26: [ OK ] SimdScalarTest.storeU (0 ms) 26: [ RUN ] SimdScalarTest.setZero 26: [ OK ] SimdScalarTest.setZero (0 ms) 26: [ RUN ] SimdScalarTest.andNot 26: [ OK ] SimdScalarTest.andNot (0 ms) 26: [ RUN ] SimdScalarTest.fma 26: [ OK ] SimdScalarTest.fma (0 ms) 26: [ RUN ] SimdScalarTest.fms 26: [ OK ] SimdScalarTest.fms (0 ms) 26: [ RUN ] SimdScalarTest.fnma 26: [ OK ] SimdScalarTest.fnma (0 ms) 26: [ RUN ] SimdScalarTest.fnms 26: [ OK ] SimdScalarTest.fnms (0 ms) 26: [ RUN ] SimdScalarTest.maskAdd 26: [ OK ] SimdScalarTest.maskAdd (0 ms) 26: [ RUN ] SimdScalarTest.maskzMul 26: [ OK ] SimdScalarTest.maskzMul (0 ms) 26: [ RUN ] SimdScalarTest.maskzFma 26: [ OK ] SimdScalarTest.maskzFma (0 ms) 26: [ RUN ] SimdScalarTest.abs 26: [ OK ] SimdScalarTest.abs (0 ms) 26: [ RUN ] SimdScalarTest.max 26: [ OK ] SimdScalarTest.max (0 ms) 26: [ RUN ] SimdScalarTest.min 26: [ OK ] SimdScalarTest.min (0 ms) 26: [ RUN ] SimdScalarTest.round 26: [ OK ] SimdScalarTest.round (0 ms) 26: [ RUN ] SimdScalarTest.trunc 26: [ OK ] SimdScalarTest.trunc (0 ms) 26: [ RUN ] SimdScalarTest.reduce 26: [ OK ] SimdScalarTest.reduce (0 ms) 26: [ RUN ] SimdScalarTest.testBits 26: [ OK ] SimdScalarTest.testBits (0 ms) 26: [ RUN ] SimdScalarTest.anyTrue 26: [ OK ] SimdScalarTest.anyTrue (0 ms) 26: [ RUN ] SimdScalarTest.selectByMask 26: [ OK ] SimdScalarTest.selectByMask (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMask 26: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 26: [ RUN ] SimdScalarTest.blend 26: [ OK ] SimdScalarTest.blend (0 ms) 26: [ RUN ] SimdScalarTest.cvtR2I 26: [ OK ] SimdScalarTest.cvtR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvttR2I 26: [ OK ] SimdScalarTest.cvttR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvtI2R 26: [ OK ] SimdScalarTest.cvtI2R (0 ms) 26: [ RUN ] SimdScalarTest.cvtF2D 26: [ OK ] SimdScalarTest.cvtF2D (0 ms) 26: [ RUN ] SimdScalarTest.cvtD2D 26: [ OK ] SimdScalarTest.cvtD2D (0 ms) 26: [ RUN ] SimdScalarTest.loadI 26: [ OK ] SimdScalarTest.loadI (0 ms) 26: [ RUN ] SimdScalarTest.loadUI 26: [ OK ] SimdScalarTest.loadUI (0 ms) 26: [ RUN ] SimdScalarTest.storeI 26: [ OK ] SimdScalarTest.storeI (0 ms) 26: [ RUN ] SimdScalarTest.storeUI 26: [ OK ] SimdScalarTest.storeUI (0 ms) 26: [ RUN ] SimdScalarTest.andNotI 26: [ OK ] SimdScalarTest.andNotI (0 ms) 26: [ RUN ] SimdScalarTest.testBitsI 26: [ OK ] SimdScalarTest.testBitsI (0 ms) 26: [ RUN ] SimdScalarTest.selectByMaskI 26: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMaskI 26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 26: [ RUN ] SimdScalarTest.blendI 26: [ OK ] SimdScalarTest.blendI (0 ms) 26: [ RUN ] SimdScalarTest.cvtB2IB 26: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 26: [ RUN ] SimdScalarTest.cvtIB2B 26: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 26: [ RUN ] SimdScalarTest.expandScalarsToTriplets 26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 26: [----------] 41 tests from SimdScalarTest (0 ms total) 26: 26: [----------] 8 tests from SimdScalarUtilTest 26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (16 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 26: [----------] 8 tests from SimdScalarUtilTest (17 ms total) 26: 26: [----------] 37 tests from SimdScalarMathTest 26: [ RUN ] SimdScalarMathTest.copysign 26: [ OK ] SimdScalarMathTest.copysign (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPair 26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 26: [ RUN ] SimdScalarMathTest.inv 26: [ OK ] SimdScalarMathTest.inv (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrt 26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdScalarMathTest.log 26: [ OK ] SimdScalarMathTest.log (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2 26: [ OK ] SimdScalarMathTest.exp2 (0 ms) 26: [ RUN ] SimdScalarMathTest.exp 26: [ OK ] SimdScalarMathTest.exp (0 ms) 26: [ RUN ] SimdScalarMathTest.erf 26: [ OK ] SimdScalarMathTest.erf (0 ms) 26: [ RUN ] SimdScalarMathTest.erfc 26: [ OK ] SimdScalarMathTest.erfc (0 ms) 26: [ RUN ] SimdScalarMathTest.sincos 26: [ OK ] SimdScalarMathTest.sincos (0 ms) 26: [ RUN ] SimdScalarMathTest.sin 26: [ OK ] SimdScalarMathTest.sin (0 ms) 26: [ RUN ] SimdScalarMathTest.cos 26: [ OK ] SimdScalarMathTest.cos (0 ms) 26: [ RUN ] SimdScalarMathTest.tan 26: [ OK ] SimdScalarMathTest.tan (0 ms) 26: [ RUN ] SimdScalarMathTest.asin 26: [ OK ] SimdScalarMathTest.asin (0 ms) 26: [ RUN ] SimdScalarMathTest.acos 26: [ OK ] SimdScalarMathTest.acos (0 ms) 26: [ RUN ] SimdScalarMathTest.atan 26: [ OK ] SimdScalarMathTest.atan (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2 26: [ OK ] SimdScalarMathTest.atan2 (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrection 26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.invSingleAccuracy 26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.logSingleAccuracy 26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.expSingleAccuracy 26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 26: [----------] 37 tests from SimdScalarMathTest (1 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 86 tests from 3 test cases ran. (19 ms total) 26: [ PASSED ] 86 tests. 26/27 Test #26: SimdUnitTests .................... Passed 0.39 sec test 27 Start 27: CompatibilityHelpersTests 27: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/compat-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 6 tests from 6 test cases. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CompatibilityHelper 27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles 27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms) 27: [----------] 1 test from CompatibilityHelper (0 ms total) 27: 27: [----------] 1 test from NotNullConstruction 27: [ RUN ] NotNullConstruction.Works 27: [ OK ] NotNullConstruction.Works (0 ms) 27: [----------] 1 test from NotNullConstruction (0 ms total) 27: 27: [----------] 1 test from NotNullCasting 27: [ RUN ] NotNullCasting.Works 27: [ OK ] NotNullCasting.Works (0 ms) 27: [----------] 1 test from NotNullCasting (0 ms total) 27: 27: [----------] 1 test from NotNullAssignment 27: [ RUN ] NotNullAssignment.Works 27: [ OK ] NotNullAssignment.Works (0 ms) 27: [----------] 1 test from NotNullAssignment (0 ms total) 27: 27: [----------] 1 test from MakeNotNull 27: [ RUN ] MakeNotNull.Works 27: [ OK ] MakeNotNull.Works (0 ms) 27: [----------] 1 test from MakeNotNull (0 ms total) 27: 27: [----------] 1 test from NotNull 27: [ RUN ] NotNull.WorksInContainers 27: [ OK ] NotNull.WorksInContainers (0 ms) 27: [----------] 1 test from NotNull (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 6 tests from 6 test cases ran. (0 ms total) 27: [ PASSED ] 6 tests. 27/27 Test #27: CompatibilityHelpersTests ........ Passed 0.47 sec 100% tests passed, 0 tests failed out of 27 Label Time Summary: GTest = 35.23 sec*proc (27 tests) MpiTest = 2.51 sec*proc (3 tests) UnitTest = 35.23 sec*proc (27 tests) Total Test time (real) = 38.80 sec touch build-openmpi dh_testdir # Build speedy, stripped-down version just for documentation generation. # Derived from admin/build-docs.sh (mkdir -p build/documentation ; cd build/documentation; \ cmake /build/gromacs-2019.1 -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None -DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DGMX_BUILD_MANUAL=ON) -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success -- Performing Test CFLAGS_PRAGMA -- Performing Test CFLAGS_PRAGMA - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_PRAGMA -- Performing Test CXXFLAGS_PRAGMA - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 8 -- Detected build CPU model - 1 -- Detected build CPU stepping - 1 -- Detected build CPU features - -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" CMake Warning at cmake/gmxTestImageMagick.cmake:69 (MESSAGE): Could not convert sample image, ImageMagick convert can not be used Call Stack (most recent call first): CMakeLists.txt:908 (GMX_TEST_IMAGEMAGICK) -- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.16", minimum required is "2.7") -- Found LATEX: /usr/bin/latex -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/documentation /usr/bin/make -j3 gmx -C build/documentation make[1]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 gmx make[2]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/documentation/CMakeFiles 68 /usr/bin/make -f CMakeFiles/Makefile2 src/programs/CMakeFiles/gmx.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/programs /build/gromacs-2019.1/build/documentation/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs_external make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp Scanning dependencies of target tng_io_obj make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c Scanning dependencies of target view_objlib make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /build/gromacs-2019.1/src/programs/view/view.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 0%] Built target view_objlib /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake --color= Scanning dependencies of target tng_io_zlib make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/compress.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 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&& /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 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/build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/inffast.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include 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-D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/inftrees.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/trees.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/uncompr.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/zutil.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_malloc.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 0%] Built target tng_io_zlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake 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-DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/bcast.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/p2p_wait.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/collective.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/profile.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/comm.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/reduce.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/event.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/event.cpp Scanning dependencies of target libgromacs_generated make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/reduce_fast.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/gather.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/scatter.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/group.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/group.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_init.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/topology.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/list.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/list.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/type.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/type.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/scan.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/numa_malloc.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/once.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/once.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 2%] Built target libgromacs_external cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 2%] Built target lmfit_objlib cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/programs /build/gromacs-2019.1/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp [ 5%] Built target tng_io_obj cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp Scanning dependencies of target mdrun_objlib make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 5%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 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-isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused 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/build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused 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/build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 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-DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src 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-Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src 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-I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/scanner.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/scanner.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/parser.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/parser.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 23%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/pargs.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/shellcompletions.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/viewit.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/atomdistribution.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/box.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/cellsizes.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/distribute.cpp In file included from /usr/include/c++/8/cmath:42, from /build/gromacs-2019.1/src/gromacs/math/vectypes.h:40, from /build/gromacs-2019.1/src/gromacs/domdec/collect.h:46, from /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:45: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:51, from /build/gromacs-2019.1/src/gromacs/domdec/collect.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:45: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:51, from /build/gromacs-2019.1/src/gromacs/domdec/collect.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:45: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlb.cpp /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/domdec/collect.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:45: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/domdec/collect.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/domdec/collect.h:47, from /build/gromacs-2019.1/src/gromacs/domdec/collect.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlbtiming.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_constraints.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_setup.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_topology.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_vsite.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dump.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/ga2la.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomset.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetdata.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/partition.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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-isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/md_enums.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/observableshistory.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpformat.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpmanager.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:57, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:57, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:58, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:297:41: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a(_GLIBCXX_MAKE_MOVE_ITERATOR(__first), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_ITERATOR(__last), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result, __alloc); ~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.h:59, from /build/gromacs-2019.1/src/gromacs/mdtypes/state.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helptopic.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/rstparser.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/boxutilities.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/mshift.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc-simd.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/pbc.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/rmpbc.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/seed.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/forcetable.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 CubicSplineTable::CubicSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp: In function 'void gmx::{anonymous}::fillSingleQuadraticSplineTableData(gmx::ArrayRef, gmx::ArrayRef, double, const std::pair&, double, std::vector*, std::vector*)': /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:157:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 fillSingleQuadraticSplineTableData(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 std::vector thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing)); ^ /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list, const std::pair&, real)': /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 QuadraticSplineTable::QuadraticSplineTable(std::initializer_list numericalInputList, ^~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp:444:47: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 fillSingleQuadraticSplineTableData(thisFuncInput.function, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ thisFuncInput.derivative, ~~~~~~~~~~~~~~~~~~~~~~~~~ thisFuncInput.spacing, ~~~~~~~~~~~~~~~~~~~~~~ range, ~~~~~~ spacing, ~~~~~~~~ &tmpFuncTableData, ~~~~~~~~~~~~~~~~~~ &tmpDerTableData); ~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/cyclecounter.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/wallcycle.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/gromacs-2019.1/src/gromacs/timing/walltime_accounting.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomprop.cpp /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef, gmx::ArrayRef, double, const std::pair&)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 throwUnlessDerivativeIsConsistentWithFunction(ArrayRef function, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp: In function 'std::vector gmx::internal::vectorSecondDerivative(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 vectorSecondDerivative(ArrayRef f, double spacing) ^~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atoms.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/atomsbuilder.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/index.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 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/build/gromacs-2019.1/src/gromacs/topology/mtop_util.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/residuetypes.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/symtab.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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-o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/topsort.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/alignedallocator.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/g96io.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmx_internal_xdr.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio-xdr.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:61, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/groio.cpp /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = PullCoordinateHistory*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = PullCoordinateHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = PullCoordinateHistory*; _Tp = PullCoordinateHistory]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = PullCoordinateHistory*; _ForwardIterator = PullCoordinateHistory*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = PullGroupHistory*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = PullGroupHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = PullGroupHistory*; _Tp = PullGroupHistory]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = PullGroupHistory*; _ForwardIterator = PullGroupHistory*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx_file_position_t*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx_file_position_t*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx_file_position_t*; _Tp = gmx_file_position_t]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx_file_position_t*; _ForwardIterator = gmx_file_position_t*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = gmx::AwhPointStateHistory*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = gmx::AwhPointStateHistory*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhPointStateHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhPointStateHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhPointStateHistory*; _Tp = gmx::AwhPointStateHistory]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::AwhPointStateHistory*; _ForwardIterator = gmx::AwhPointStateHistory*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.h:44, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp:39: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx_file_position_t*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx_file_position_t*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx_file_position_t*; _Tp = gmx_file_position_t]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx_file_position_t*; _ForwardIterator = gmx_file_position_t*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.h:44, from /build/gromacs-2019.1/src/gromacs/fileio/gmxfio.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/libxdrf.cpp In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.h:43, from /build/gromacs-2019.1/src/gromacs/fileio/checkpoint.cpp:40: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhBiasHistory*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhBiasHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhBiasHistory*; _Tp = gmx::AwhBiasHistory]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::AwhBiasHistory*; _ForwardIterator = gmx::AwhBiasHistory*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/matio.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/md5.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/mtxio.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/oenv.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/pdbio.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/readinp.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/timecontrol.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tngio.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tpxio.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trrio.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trxio.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/vmdio.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/warninp.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/writeps.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xdrd.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xtcio.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xvgr.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/__/external/vmd_molfile/vmddlopen.c.o -c /build/gromacs-2019.1/src/external/vmd_molfile/vmddlopen.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/output.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/commandline/filenm.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/output.cpp:43: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = PullCoordinateHistory*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = PullCoordinateHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = PullCoordinateHistory*; _Tp = PullCoordinateHistory]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = PullCoordinateHistory*; _ForwardIterator = PullCoordinateHistory*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = PullGroupHistory*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = PullGroupHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = PullGroupHistory*; _Tp = PullGroupHistory]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = PullGroupHistory*; _ForwardIterator = PullGroupHistory*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pull_rotation.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp In file included from /usr/include/c++/8/cmath:42, from /build/gromacs-2019.1/src/gromacs/math/vectypes.h:40, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:51, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:51, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = pull_coord_work_t*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = pull_coord_work_t*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = pull_coord_work_t*; _Tp = pull_coord_work_t]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = pull_coord_work_t*; _ForwardIterator = pull_coord_work_t*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator*>; _ForwardIterator = gmx::BasicVector*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator*>; _ForwardIterator = gmx::BasicVector*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator*>; _ForwardIterator = gmx::BasicVector*; _Tp = gmx::BasicVector]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::BasicVector*; _ForwardIterator = gmx::BasicVector*; _Allocator = std::allocator >]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:51, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = ComSums*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:51, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = ComSums*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = ComSums*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = ComSums*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = ComSums*; _Tp = ComSums]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = ComSums*; _ForwardIterator = ComSums*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:51, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = pull_group_work_t*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = pull_group_work_t*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = pull_group_work_t*; _Tp = pull_group_work_t]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = pull_group_work_t*; _ForwardIterator = pull_group_work_t*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:55, from /build/gromacs-2019.1/src/gromacs/pulling/pull.h:58, from /build/gromacs-2019.1/src/gromacs/pulling/pull.cpp:39: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator*>; _ForwardIterator = gmx::BasicVector*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator*>; _ForwardIterator = gmx::BasicVector*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator*>; _ForwardIterator = gmx::BasicVector*; _Tp = gmx::BasicVector]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::BasicVector*; _ForwardIterator = gmx::BasicVector*; _Allocator = std::allocator >]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator*>' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:49, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:49, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/awh.cpp In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp:45: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/bias.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp: In function 'double gmx::{anonymous}::gaussianGeometryFactor(gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:169:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double gaussianGeometryFactor(gmx::ArrayRef xArray) ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:70: /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h: In member function 'void gmx::CorrelationGrid::addData(int, double, gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:102:14: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void addData(int pointIndex, ^~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.h:53, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:47: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.h:53, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:47: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.h:53, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.h:53, from /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:54, from /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::DimParams*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::DimParams*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::DimParams*; _Tp = gmx::DimParams]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/bias.h:55, from /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:463:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__x.begin(), __x.end(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ this->_M_impl._M_start, ~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biassharing.cpp /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void Bias::updateForceCorrelationGrid(gmx::ArrayRef probWeightNeighbor, ^~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 updateForceCorrelationGrid(probWeightNeighbor, t); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tempForce_, biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:67, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::DimParams*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::DimParams*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::DimParams*; _Tp = gmx::DimParams]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:463:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__x.begin(), __x.end(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ this->_M_impl._M_start, ~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:67, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::GridAxis*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::GridAxis*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::GridAxis*; _Tp = gmx::GridAxis]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:463:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__x.begin(), __x.end(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ this->_M_impl._M_start, ~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:67, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::GridPoint*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::GridPoint*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::GridPoint*; _Tp = gmx::GridPoint]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gmx::GridPoint; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:463:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__x.begin(), __x.end(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ this->_M_impl._M_start, ~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:67, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::DimParams*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::DimParams*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::DimParams*; _Tp = gmx::DimParams]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::DimParams*; _ForwardIterator = gmx::DimParams*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:67, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhBiasHistory*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhBiasHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhBiasHistory*; _Tp = gmx::AwhBiasHistory]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::AwhBiasHistory*; _ForwardIterator = gmx::AwhBiasHistory*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::BiasCoupledToSystem*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::BiasCoupledToSystem*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::BiasCoupledToSystem*; _Tp = gmx::BiasCoupledToSystem]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::BiasCoupledToSystem*; _ForwardIterator = gmx::BiasCoupledToSystem*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.h:69, from /build/gromacs-2019.1/src/gromacs/awh/awh.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biaswriter.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gmx::Bias, std::vector >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::sumOverSimulations(gmx::ArrayRef, const gmx_multisim_t*)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void sumOverSimulations(gmx::ArrayRef arrayRef, ^~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'double gmx::{anonymous}::freeEnergyMinimumValue(gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:189:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double freeEnergyMinimumValue(gmx::ArrayRef pointState) ^~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector&, const gmx::Grid&, int, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::calcUmbrellaForceAndPotential(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef, const gmx::BiasParams&)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void updateTargetDistribution(gmx::ArrayRef pointState, ^~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::sumOverSimulations(gmx::ArrayRef, const t_commrec*, const gmx_multisim_t*) [with T = double]': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:128:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void sumOverSimulations(gmx::ArrayRef arrayRef, ^~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, gmx::ArrayRef) const': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::calcConvolvedForce(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:463:38: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forceFromNeighbor); ~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleProbabilityWeights(const Grid &grid, ^~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:71, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/coordstate.h:55, from /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:47: /usr/include/c++/8/bits/predefined_ops.h: In function 'bool __gnu_cxx::__ops::_Val_less_iter::operator()(_Value&, _Iterator) const [with _Value = const double; _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/predefined_ops.h:89:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 operator()(_Value& __val, _Iterator __it) const ^~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef, double)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void BiasState::sampleCoordAndPmf(const Grid &grid, ^~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:66, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/coordstate.h:55, from /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:47: /usr/include/c++/8/bits/stl_iterator_base_funcs.h: In function 'typename std::iterator_traits<_Iterator>::difference_type std::__distance(_RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __distance(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_iterator_base_funcs.h: In function 'typename std::iterator_traits<_Iterator>::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 distance(_InputIterator __first, _InputIterator __last) ^~~~~~~~ /usr/include/c++/8/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_iterator_base_funcs.h:141:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__distance(__first, __last, ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:49: /usr/include/c++/8/bits/stl_algo.h: In function '_ForwardIterator std::__upper_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2039:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __upper_bound(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2039:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2039:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2045:42: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _DistanceType __len = std::distance(__first, __last); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function '_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]': /usr/include/c++/8/bits/stl_algo.h:2077:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 upper_bound(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2077:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2086:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__upper_bound(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp: In function 'int gmx::{anonymous}::getSampleFromDistribution(gmx::ArrayRef, int64_t, int64_t, int64_t)': /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:97:5: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 int getSampleFromDistribution(ArrayRef distr, ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:123:109: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 int sample = std::upper_bound(cumulativeDistribution.begin(), cumulativeDistribution.end() - 1, value) - cumulativeDistribution.begin(); ^ /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 CoordState::sampleUmbrellaGridpoint(const Grid &grid, ^~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.h:57, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Allocator = gmx::Allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:267:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:267:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = gmx::Allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector&, const gmx::Grid&, gmx::ArrayRef, gmx::ArrayRef, int64_t, int64_t, int)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double BiasState::moveUmbrella(const std::vector &dimParams, ^~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:487:38: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::sumPmf(gmx::ArrayRef, int, const t_commrec*, const gmx_multisim_t*)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:150:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void sumPmf(gmx::ArrayRef pointState, ^~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.h:57, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:47: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = gmx::AwhPointStateHistory*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algobase.h:61, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const gmx::CorrelationBlockData*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = gmx::CorrelationBlockData*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:62, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_construct.h: In static member function 'static void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]': /usr/include/c++/8/bits/stl_construct.h:105:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __destroy(_ForwardIterator __first, _ForwardIterator __last) ^~~~~~~~~ /usr/include/c++/8/bits/stl_construct.h:105:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_construct.h: In function 'void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_construct.h:127:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Destroy(_ForwardIterator __first, _ForwardIterator __last) ^~~~~~~~ /usr/include/c++/8/bits/stl_construct.h:127:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_construct.h:137:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy_aux<__has_trivial_destructor(_Value_type)>:: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __destroy(__first, __last); ~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_construct.h: In function 'void std::_Destroy(_ForwardIterator, _ForwardIterator, std::allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gmx::CorrelationBlockData]': /usr/include/c++/8/bits/stl_construct.h:203:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Destroy(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~ /usr/include/c++/8/bits/stl_construct.h:203:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_construct.h:203:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_construct.h:206:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Destroy(__first, __last); ~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.h:57, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:47: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.h:57, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:61, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.h:57, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:47: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = gmx::AwhPointStateHistory*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.h:57, from /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhPointStateHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const gmx::CorrelationBlockData::CoordData*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhPointStateHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AwhPointStateHistory*; _Tp = gmx::AwhPointStateHistory]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = gmx::CorrelationBlockData::CoordData*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::AwhPointStateHistory*; _ForwardIterator = gmx::AwhPointStateHistory*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData::CoordData*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData::CoordData*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData::CoordData*; _Tp = gmx::CorrelationBlockData::CoordData]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gmx::CorrelationBlockData::CoordData; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:463:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__x.begin(), __x.end(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ this->_M_impl._M_start, ~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gmx::CorrelationBlockData::CoordData; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gmx::CorrelationBlockData::CoordData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:463:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__x.begin(), __x.end(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ this->_M_impl._M_start, ~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector*)': /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData*; _Tp = gmx::CorrelationBlockData]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:463:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__x.begin(), __x.end(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ this->_M_impl._M_start, ~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationgrid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algobase.h:61, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:49, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:49, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const gmx::CorrelationBlockData::CoordData*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = gmx::CorrelationBlockData::CoordData*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:49, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:49, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:49, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData::CoordData*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData::CoordData*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData::CoordData*; _Tp = gmx::CorrelationBlockData::CoordData]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gmx::CorrelationBlockData::CoordData; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gmx::CorrelationBlockData::CoordData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:49, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/grid.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:49, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = gmx::CorrelationBlockDataHistory*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:49, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = gmx::CorrelationBlockDataHistory*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/utility/stringutil.h:50, from /build/gromacs-2019.1/src/gromacs/gmxlib/network.h:48, from /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp:52: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::CorrelationBlockDataHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::CorrelationBlockDataHistory*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::CorrelationBlockDataHistory*; _Tp = gmx::CorrelationBlockDataHistory]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::CorrelationBlockDataHistory*; _ForwardIterator = gmx::CorrelationBlockDataHistory*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp In file included from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h: In member function 'void gmx::CorrelationBlockData::addData(double, gmx::ArrayRef)': /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:116:14: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void addData(double weight, ^~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:61, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = gmx::CorrelationBlockData::CoordData*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const gmx::CorrelationBlockData::CoordData*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData::CoordData*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData::CoordData*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gmx::CorrelationBlockData::CoordData*; _Tp = gmx::CorrelationBlockData::CoordData]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gmx::CorrelationBlockData::CoordData; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gmx::CorrelationBlockData::CoordData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:60, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef, bool, double)': /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 void CorrelationTensor::addData(double weight, ^~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:267:19: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 bd.addData(weight, data); ~~~~~~~~~~^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:273:34: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 blockDataList_.back().addData(weight, data); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::CorrelationBlockData*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector&, gmx::ArrayRef, FILE*)': /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 double HistogramSize::newHistogramSize(const BiasParams ¶ms, ^~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::CorrelationBlockData*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::CorrelationBlockData*; _Tp = gmx::CorrelationBlockData]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::CorrelationBlockData*; _ForwardIterator = gmx::CorrelationBlockData*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.h:51, from /build/gromacs-2019.1/src/gromacs/awh/correlationtensor.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/pointstate.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/read-params.cpp In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:57, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::GridAxis*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::GridAxis*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::GridAxis*; _Tp = gmx::GridAxis]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::GridAxis*; _ForwardIterator = gmx::GridAxis*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/support.cpp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = std::move_iterator; _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/awh/dimparams.h:52, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:60, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::reserve(std::vector<_Tp, _Alloc>::size_type) [with _Tp = gmx::GridAxis; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:74:12: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__n, ^~~~~ In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/awh/grid.h:57, from /build/gromacs-2019.1/src/gromacs/awh/grid.cpp:47: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::GridPoint*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::GridPoint*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::GridPoint*; _Tp = gmx::GridPoint]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::GridPoint*; _ForwardIterator = gmx::GridPoint*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imd.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imdsocket.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/anadih.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/binsearch.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/cmat.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/dens_filter.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c 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cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/integrate.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/polynomials.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /build/gromacs-2019.1/src/gromacs/statistics/statistics.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/abstractdata.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/analysisdata.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/arraydata.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/dataframe.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/datamodule.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/datamodulemanager.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/dataproxy.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/datastorage.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/average.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/displacement.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/frameaverager.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/lifetime.cpp In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/frameaverager.h:45, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/frameaverager.cpp:44: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AnalysisDataFrameAverager::AverageItem*; bool _TrivialValueTypes = false]': /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AnalysisDataFrameAverager::AverageItem*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gmx::AnalysisDataFrameAverager::AverageItem*; _Tp = gmx::AnalysisDataFrameAverager::AverageItem]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gmx::AnalysisDataFrameAverager::AverageItem*; _ForwardIterator = gmx::AnalysisDataFrameAverager::AverageItem*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/modules/plot.cpp In file included from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:53: /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h: In constructor 'gmx::AnalysisDataFrameLocalDataSetHandle::AnalysisDataFrameLocalDataSetHandle(gmx::ArrayRef) [with ValueType = long long int]': /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h:72:18: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 explicit AnalysisDataFrameLocalDataSetHandle(ArrayRef values) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h: In member function 'gmx::AnalysisDataFrameLocalDataHandle::DataSetHandle gmx::AnalysisDataFrameLocalDataHandle::dataSet(int) [with ValueType = long long int]': /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h:138:80: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 subArray(firstIndex, lastIndex-firstIndex)); ^ /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h: In constructor 'gmx::AnalysisDataFrameLocalDataSetHandle::AnalysisDataFrameLocalDataSetHandle(gmx::ArrayRef) [with ValueType = double]': /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h:72:18: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 explicit AnalysisDataFrameLocalDataSetHandle(ArrayRef values) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h: In member function 'gmx::AnalysisDataFrameLocalDataHandle::DataSetHandle gmx::AnalysisDataFrameLocalDataHandle::dataSet(int) [with ValueType = double]': /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h:138:80: note: parameter passing for argument of type 'gmx::ArrayRef' changed in GCC 7.1 subArray(firstIndex, lastIndex-firstIndex)); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:44: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = long long int*; _Container = std::vector >]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:44: /usr/include/c++/8/bits/stl_algobase.h: In function 'void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = long long int]': /usr/include/c++/8/bits/stl_algobase.h:724:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 fill(_ForwardIterator __first, _ForwardIterator __last, const _Tp& __value) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:724:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 In file included from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:53: /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h: In function 'void gmx::AnalysisDataFrameLocalDataHandle::clear() [with ValueType = long long int]': /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h:127:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 std::fill(values_->begin(), values_->end(), ValueType()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:44: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector >]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:44: /usr/include/c++/8/bits/stl_algobase.h: In function 'void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Tp = double]': /usr/include/c++/8/bits/stl_algobase.h:724:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 fill(_ForwardIterator __first, _ForwardIterator __last, const _Tp& __value) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:724:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 In file included from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:53: /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h: In function 'void gmx::AnalysisDataFrameLocalDataHandle::clear() [with ValueType = double]': /build/gromacs-2019.1/src/gromacs/analysisdata/framelocaldata.h:127:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 std::fill(values_->begin(), values_->end(), ValueType()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/centerofmass.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/compiler.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:44: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = long long int*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:44: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = long long int*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:44: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = long long int*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = long long int*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = long long int*; _Tp = long long int]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = long long int*; _ForwardIterator = long long int*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:44: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.h:46, from /build/gromacs-2019.1/src/gromacs/analysisdata/modules/histogram.cpp:44: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/evaluate.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/indexutil.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/mempool.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/nbsearch.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c 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/build/gromacs-2019.1/src/gromacs/selection/sm_simple.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/symrec.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysissettings.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/angle.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/distance.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysismodule.h:47, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.h:45, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysismodule.h:47, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.h:45, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysismodule.h:47, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.h:45, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/analysismodule.h:49, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.h:45, from /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/pairdist.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/modules/select.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/force.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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-DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/lincs.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/md_support.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin_bar.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdsetup.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/stl_tree.h:63, from /usr/include/c++/8/map:60, from /build/gromacs-2019.1/src/gromacs/trajectory/energyframe.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/ebin.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp:39: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_tree.h:63, from /usr/include/c++/8/map:60, from /build/gromacs-2019.1/src/gromacs/trajectory/energyframe.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/ebin.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.h:43, from /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp:39: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/topology/idef.h:43, from /build/gromacs-2019.1/src/gromacs/mdtypes/enerdata.h:39, from /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.h:44, from /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp:39: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/membed.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_atomdata.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nsgrid.cpp cd 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/build/gromacs-2019.1/src/gromacs/mdlib/qm_mopac.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_orca.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src 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/build/gromacs-2019.1/src/gromacs/mdlib/resethandler.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rf_util.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src 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-g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/shake.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/sighandler.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src 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/build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/simulationsignal.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/splitter.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/stat.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/stophandler.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tgroup.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/updategroups.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/updategroupscog.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/algorithm:61, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/update.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:39: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:61, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:46, from /build/gromacs-2019.1/src/gromacs/mdlib/update.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:39: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/mdlib/update.h:40, from /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp:39: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/vcm.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src 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/build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/integrator.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/integrator.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/logging.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/multisim.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/replicaexchange.cpp In file included from /usr/include/c++/8/cmath:42, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:49: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/algorithm:61, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:53: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:61, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:53: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp:54: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/handlerestart.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/mdmodules.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractoption.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractsection.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/behaviorcollection.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/options.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsassigner.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsection.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsvisitor.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/timeunitmanager.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/treesupport.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:49, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/manager.cpp In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:49, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = std::move_iterator; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::reserve(std::vector<_Tp, _Alloc>::size_type) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:74:12: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__n, ^~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/restraintmdmodule.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:49, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = long long int*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:49, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = long long int*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = long long int*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = long long int*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = long long int*; _Tp = long long int]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = long long int*; _ForwardIterator = long long int*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator > >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = std::move_iterator; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.h:50, from /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp:44: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::reserve(std::vector<_Tp, _Alloc>::size_type) [with _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:74:12: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__n, ^~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/taskassignment.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/usergpuids.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectory/energyframe.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectory/trajectoryframe.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /build/gromacs-2019.1/src/gromacs/mimic/MimicUtils.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/gromacs-2019.1/build/documentation/src/gromacs/utility/baseversion-gen.cpp In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:53, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.h:39, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp:37: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/memory:62, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:53, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.h:39, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp:37: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/memory:65, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:53, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.h:39, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp:37: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /build/gromacs-2019.1/src/gromacs/math/paddedvector.h:47, from /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.h:55, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.h:39, from /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs.so.4 -o ../../lib/libgromacs.so.4.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp -Wl,-rpath,"\$ORIGIN/../lib" /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -lm /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.4.0.0 ../../lib/libgromacs.so.4 ../../lib/libgromacs.so make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [100%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/programs /build/gromacs-2019.1/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= Scanning dependencies of target gmx make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -o CMakeFiles/gmx.dir/gmx.cpp.o -c /build/gromacs-2019.1/src/programs/gmx.cpp cd /build/gromacs-2019.1/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /build/gromacs-2019.1/src/programs/legacymodules.cpp cd /build/gromacs-2019.1/build/documentation/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o -o ../../bin/gmx -Wl,-rpath,"\$ORIGIN/../lib" ../../lib/libgromacs.so.4.0.0 -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [100%] Built target gmx make[3]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[1]: Leaving directory '/build/gromacs-2019.1/build/documentation' # 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/build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 0%] Built target doxygen-version /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build [ 2%] Built target tng_io_obj make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_zlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 4%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= [ 4%] Built target tng_io_zlib /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/programs /build/gromacs-2019.1/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 4%] Built target lmfit_objlib /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake --color= [ 4%] Built target mdrun_objlib /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake --color= Scanning dependencies of target sphinx-input-rst make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/plots/xvgr.png /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/plots/xvgr.png Scanning dependencies of target sphinx-image-conversion make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/sphinx-image-conversion-timestamp.txt make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 19%] Built target libgromacs_generated /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/docs/conf-vars.py.cmakein -D VERSION_OUT=/build/gromacs-2019.1/build/documentation/docs/sphinx-input/conf-vars.py -D SPHINX_EXTENSION_PATH=/build/gromacs-2019.1/docs -D RELENG_PATH= -D IMAGE_CONVERT_STRING=impossible -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=1.6.1 -D CMAKE_MINIMUM_REQUIRED_VERSION=3.4.3 -D REQUIRED_CUDA_VERSION=7.0 -D REQUIRED_OPENCL_MIN_VERSION=1.2 -D REQUIRED_CUDA_COMPUTE_CAPABILITY=3.0 -D REGRESSIONTEST_VERSION=2019.1 -D SOURCE_MD5SUM=unknown -D REGRESSIONTEST_MD5SUM_STRING=unknown -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=Please reference this documentation as https://doi.org/10.5281/zenodo.2564761." -D "GMX_SOURCE_DOI_STRING=To cite the source code for this release, please cite https://doi.org/10.5281/zenodo.2564764." -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-xml.dir/DependInfo.cmake --color= [ 19%] Built target sphinx-image-conversion /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/sphinx-input/conf-vars.py Scanning dependencies of target doxygen-xml make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/gromacs-2019.1/build/documentation/docs/doxygen/depgraphs cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/index.rst cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=xml -P RunDoxygen.cmake cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/download.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/download.rst NOTE: You are using Doxygen version 1.8.13. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/conf.py /build/gromacs-2019.1/build/documentation/docs/sphinx-input/conf.py cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/links.dat /build/gromacs-2019.1/build/documentation/docs/sphinx-input/links.dat cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/build-system.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/build-system.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/change-management.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/change-management.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/commitstyle.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/commitstyle.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/documentation-generation.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/documentation-generation.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/contribute.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/contribute.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/doxygen.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/doxygen.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/error-handling.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/error-handling.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/formatting.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/formatting.rst make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/gmxtree.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/gmxtree.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/includestyle.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/includestyle.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/jenkins.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/jenkins.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/known-issues.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/known-issues.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/language-features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/language-features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/naming.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/naming.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/overview.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/overview.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/physical_validation.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/physical_validation.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/redmine-states.png /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/redmine-states.png cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/relocatable-binaries.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/relocatable-binaries.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/reportstyle.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/reportstyle.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/style.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/style.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/testutils.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/testutils.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/tools.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/tools.rst make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/uncrustify.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/uncrustify.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/fragments/doxygen-links.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/fragments/doxygen-links.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/how-to/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/how-to/beginners.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/beginners.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/how-to/topology.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/topology.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/how-to/special.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/special.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/how-to/visualize.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/visualize.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/install-guide/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/install-guide/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/index.rst make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/2019.1.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/2019.1.rst [ 83%] Built target libgromacs cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/highlights.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/highlights.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/performance.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/performance.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/tools.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/tools.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/bugs-fixed.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/bugs-fixed.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/removed-functionality.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/removed-functionality.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/deprecated-functionality.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/deprecated-functionality.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/portability.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/portability.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/miscellaneous.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/miscellaneous.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.6.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.6.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.5.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.5.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.4.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.4.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.3.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.3.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.2.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.2.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.1.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.1.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/highlights.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/highlights.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/features.rst /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/programs /build/gromacs-2019.1/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/performance.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/performance.rst make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/tools.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/tools.rst [ 83%] Built target gmx cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/bugs-fixed.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/bugs-fixed.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/removed-features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/removed-features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/portability.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/portability.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/miscellaneous.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/miscellaneous.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/2016.5.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/2016.5.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/2016.4.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/2016.4.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/2016.3.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/2016.3.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/2016.2.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/2016.2.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/2016.1.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/2016.1.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/highlights.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/highlights.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/new-features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/new-features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/performance.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/performance.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/tools.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/tools.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/bugs-fixed.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/bugs-fixed.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/removed-features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/removed-features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/miscellaneous.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/miscellaneous.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/older/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/older/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/cmdline.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/cmdline.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/cutoff-schemes.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/cutoff-schemes.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/deprecation-policy.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/deprecation-policy.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/environment-variables.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/environment-variables.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/faq.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/faq.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/floating-point.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/floating-point.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/flow.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/flow.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/force-fields.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/force-fields.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/getting-started.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/getting-started.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/managing-simulations.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/managing-simulations.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/mdp-options.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/mdp-options.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/mdrun-features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/mdrun-features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/mdrun-performance.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/mdrun-performance.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/run-time-errors.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/run-time-errors.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/security.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/security.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/system-preparation.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/system-preparation.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/terminology.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/terminology.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/releng/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/releng/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/releng/jenkins-howto.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/releng/jenkins-howto.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/releng/jenkins-ui.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/releng/jenkins-ui.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/preface.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/preface.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/introduction.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/introduction.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/definitions.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/definitions.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/particle-type.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/parameter-files.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/parameter-files.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/molecule-definition.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/constraint-algorithm-section.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/constraint-algorithm-section.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/pdb2gmx-input-files.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/topology-file-formats.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/force-field-organization.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/force-field-organization.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/file-formats.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/file-formats.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/run-parameters.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/run-parameters.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/details.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/details.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/averages.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/averages.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/references.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/references.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/plots/peregrine.png /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/plots/peregrine.png cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/plots/adress.png /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/plots/adress.png cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/plots/plotje.png /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/plots/plotje.png cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/sphinx-input-rst-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 93%] Built target sphinx-input-rst /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake --color= Scanning dependencies of target sphinx-input make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 93%] Built target sphinx-input /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake --color= Scanning dependencies of target sphinx-programs make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/sphinx-input && /usr/bin/cmake -E make_directory onlinehelp cd /build/gromacs-2019.1/build/documentation/docs/sphinx-input && /build/gromacs-2019.1/build/documentation/bin/gmx -quiet help -export rst cd /build/gromacs-2019.1/build/documentation/docs/sphinx-input && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/sphinx-programs-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 95%] Built target sphinx-programs /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/webpage-sphinx.dir/DependInfo.cmake --color= Scanning dependencies of target webpage-sphinx make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E make_directory /build/gromacs-2019.1/build/documentation/docs/sphinx-input/_static cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/sphinx-build -q -E -b html -w sphinx-html.log -d /build/gromacs-2019.1/build/documentation/docs/_doctrees /build/gromacs-2019.1/build/documentation/docs/sphinx-input /build/gromacs-2019.1/build/documentation/docs/html The following warnings were produced by Doxygen: /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:195: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:205: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(const EmptyArrayRef&)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:195: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:205: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(const EmptyArrayRef&)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/fileio/warninp.h:117: warning: @copybrief or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/gromacs-2019.1/src/gromacs/fileio/warninp.h:117: warning: @copydetails or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/gromacs-2019.1/src/gromacs/fileio/warninp.h:117: warning: @copybrief or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/gromacs-2019.1/src/gromacs/fileio/warninp.h:117: warning: @copydetails or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `g' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `m' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `x' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `t' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `e' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `s' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `t' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `:' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/doxygen-xml-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 96%] Built target doxygen-xml /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-user.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/dep-graphs-dot.dir/DependInfo.cmake --color= Scanning dependencies of target doxygen-user Scanning dependencies of target dep-graphs-dot make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/build /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/gromacs-2019.1/build/documentation/docs/doxygen/depgraphs make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/python2.7 /build/gromacs-2019.1/docs/doxygen/graphbuilder.py -S /build/gromacs-2019.1 -B /build/gromacs-2019.1/build/documentation --ignore-cycles /build/gromacs-2019.1/docs/doxygen/cycle-suppressions.txt -o /build/gromacs-2019.1/build/documentation/docs/doxygen/depgraphs cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=user -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.8.13. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... Scanning source tree... Reading source files... /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/index.rst:25: WARNING: toctree contains reference to nonexisting document u'reference-manual/algorithms' /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/index.rst:25: WARNING: toctree contains reference to nonexisting document u'reference-manual/functions' /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/index.rst:25: WARNING: toctree contains reference to nonexisting document u'reference-manual/special' /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/index.rst:25: WARNING: toctree contains reference to nonexisting document u'reference-manual/analysis' Reading Doxygen XML files... libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp:5145: warning: documented symbol `if *lworkl(* ncv<< 3)' was not declared or defined. /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp:5352: warning: documented symbol `if *rvec(* ncv<< 3)' was not declared or defined. /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/doxygen-user-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 96%] Built target doxygen-user /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/special.rst:84: WARNING: undefined label: ff (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/definitions.rst:284: WARNING: undefined label: virial (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/details.rst:241: WARNING: undefined label: lj (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/details.rst:241: WARNING: undefined label: coul (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/details.rst:255: WARNING: undefined label: lj (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/details.rst:257: WARNING: undefined label: coul (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/introduction.rst:306: WARNING: undefined label: em (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies.rst:4: WARNING: undefined label: ff (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:79: WARNING: undefined label: fecalc (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:100: WARNING: undefined label: fecalc (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:100: WARNING: undefined label: dgimplement (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:134: WARNING: undefined label: groupconcept (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst:63: WARNING: undefined label: virtualsites (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst:68: WARNING: undefined label: virtualsites (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst:56: WARNING: undefined label: defaultgroups (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst:151: WARNING: undefined label: charmmff (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:552: WARNING: undefined label: positionrestraint (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:556: WARNING: undefined label: dihedralrestraint (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:563: WARNING: equation not found: eqndphi /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:563: WARNING: equation not found: eqndihre /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:566: WARNING: equation not found: eqndihre /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:569: WARNING: equation not found: eqndihre /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:577: WARNING: undefined label: groupconcept (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:577: WARNING: undefined label: usinggroups (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:716: WARNING: undefined label: positionrestraint (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:724: WARNING: undefined label: fecalc (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:724: WARNING: undefined label: feia (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:865: WARNING: undefined label: pull (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/mdp-options.rst:3066: WARNING: undefined label: electric fields (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/terminology.rst:72: WARNING: undefined label: pbc (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/terminology.rst:135: WARNING: undefined label: temp-coupling (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/terminology.rst:370: WARNING: undefined label: md (if the link has no caption the label must precede a section header) Writing graphs... make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 97%] Built target webpage-sphinx cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/dep-graphs-dot-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 98%] Built target dep-graphs-dot /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-full.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-lib.dir/DependInfo.cmake --color= Scanning dependencies of target doxygen-full make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/build Scanning dependencies of target doxygen-lib make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/gromacs-2019.1/build/documentation/docs/doxygen/depgraphs make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/gromacs-2019.1/build/documentation/docs/doxygen/depgraphs cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=full -P RunDoxygen.cmake cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=lib -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.8.13. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... NOTE: You are using Doxygen version 1.8.13. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp:5145: warning: documented symbol `if *lworkl(* ncv<< 3)' was not declared or defined. /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp:5352: warning: documented symbol `if *rvec(* ncv<< 3)' was not declared or defined. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'classhelpers.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/doxygen-lib-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 98%] Built target doxygen-lib The following warnings were produced by Doxygen: warning: Included by graph for 'gmxpre.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Include graph for 'runner.cpp' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'arrayref.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'classhelpers.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'exceptions.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'fatalerror.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'gmxassert.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'smalloc.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'stringutil.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'refdata.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testasserts.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `g' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `m' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `x' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `t' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `e' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `s' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `t' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< bool > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< double > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< float > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< int64_t > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/doxygen-full-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [100%] Built target doxygen-full /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-all.dir/DependInfo.cmake --color= Scanning dependencies of target doxygen-all make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'docs/doxygen/CMakeFiles/doxygen-all.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [100%] Built target doxygen-all /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/webpage.dir/DependInfo.cmake --color= Scanning dependencies of target webpage make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E echo "webpage was built, but with the following limitations:" webpage was built, but with the following limitations: cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E echo " - Reference PDF manual was not built, so links to it do not work" - Reference PDF manual was not built, so links to it do not work make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [100%] Built target webpage make[3]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[1]: Leaving directory '/build/gromacs-2019.1/build/documentation' dh_testdir dh_testroot dh_prep -pgromacs dh_installdirs -pgromacs /usr/bin/make -j3 -C build/basic install DESTDIR=/build/gromacs-2019.1/debian/gromacs make[1]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic/CMakeFiles /build/gromacs-2019.1/build/basic/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 1%] Built target tng_io_obj /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 5%] Built target libgromacs_external /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 5%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs /build/gromacs-2019.1/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= [ 21%] Built target libgromacs_generated /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs /build/gromacs-2019.1/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 23%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 24%] Built target view_objlib [ 24%] Built target mdrun_test_objlib make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 98%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/share/template /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/share/template /build/gromacs-2019.1/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs /build/gromacs-2019.1/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'share/template/CMakeFiles/template.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target template [100%] Built target gmx make[2]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/basic' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/basic' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-traj.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-wham.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-view.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-freevolume.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dos.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rms.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sham.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mdrun.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-msd.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-genion.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mindist.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-vanhove.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-covar.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sans.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-bundle.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-helix.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-morph.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-make_ndx.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-do_dssp.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-h2order.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rdf.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dyndom.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sasa.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dump.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dielectric.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-pme_error.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-nmens.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-cluster.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-trajectory.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-eneconv.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-energy.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-saxs.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-make_edi.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-trjorder.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-enemat.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-insert-molecules.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-anadock.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-spol.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-select.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-polystat.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-distance.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-hbond.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rmsdist.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-spatial.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mk_angndx.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-trjcat.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-saltbr.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-helixorient.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-hydorder.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-convert-tpr.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-principal.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-filter.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-tune_pme.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rotacf.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-bar.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-analyze.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-pdb2gmx.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-order.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-potential.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-x2top.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-confrms.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-genconf.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-density.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rmsf.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-nmr.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-grompp.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-gyrate.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-help.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-densmap.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-editconf.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-tcaf.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-nmeig.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-check.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-genrestr.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-nmtraj.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rotmat.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-solvate.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dipoles.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sigeps.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-disre.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mdmat.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-chi.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rama.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-anaeig.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-velacc.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-wheel.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-clustsize.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-angle.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-xpm2ps.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sorient.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-gangle.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-current.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dyecoupl.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-lie.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-trjconv.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-densorder.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-awh.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-report-methods.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-pairdist.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/README.tutor -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/README_FreeEnergyModifications.txt -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/spc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ffoplsaa-n.tst -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/spc216.gro -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/spc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber94.ff -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber94.ff/spc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber94.ff/rna.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber94.ff/dna.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber94.ff/ions.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber94.ff/dna.rtp -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.arn -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber96.ff/spce.itp -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ions.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.arn -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/spce.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.arn -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/flexspc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/flexspce.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/dgsolv.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Installing: 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Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ffG43a2.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/table6-8.xvg -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ca-shift.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/specbond.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ps.m2p -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/xlateat.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/table6-12.xvg -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/CMakeLists.txt -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/README -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/template.cpp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/Makefile.pkg -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/cmake/FindGROMACS.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.bash -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.zsh -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.csh -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/demux.pl -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/xplor2gmx.pl -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/version.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs.so.4.0.0 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs.so.4 -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs.so.4.0.0" to "$ORIGIN/../lib/arm-linux-gnueabihf" -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs.so -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/pkgconfig/libgromacs.pc -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs/libgromacs.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs/libgromacs-release.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs/gromacs-config.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs/gromacs-config-version.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdlib/simulationsignal.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlinehelpwriter.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineinit.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlinemodule.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineoptionsmodule.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineparser.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineprogramcontext.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/filenm.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/pargs.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/viewit.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fft/fft.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/gpu_utils/hostallocator.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/linearalgebra/eigensolver.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/linearalgebra/matrix.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/linearalgebra/sparsematrix.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/3dtransforms.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/arrayrefwithpadding.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/do_fit.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/functions.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/gmxcomplex.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/units.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/utilities.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/vec.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/vectypes.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/paddedvector.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/inputrec.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/mdatom.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/md_enums.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/state.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/abstractoption.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/abstractsection.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/basicoptions.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/filenameoption.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/filenameoptionmanager.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ioptionsbehavior.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ioptionscontainer.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ioptionscontainerwithsections.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/isectionstorage.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ivaluestore.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/optionfiletype.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/optionflags.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/options.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/optionsection.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/repeatingsection.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/timeunitmanager.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/valuestore.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/ishift.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/pbc.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/rmpbc.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/exponentialdistribution.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/gammadistribution.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/normaldistribution.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/seed.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/tabulatednormaldistribution.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/threefry.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/uniformintdistribution.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/uniformrealdistribution.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/timing/wallcycle.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/timing/walltime_accounting.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/atomprop.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/atoms.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/block.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/forcefieldparameters.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/idef.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/ifunc.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/index.h -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/gmxfio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/matio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/mtxio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/oenv.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/pdbio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/rgb.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/tpxio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/trrio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/trxio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xdr_datatype.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xtcio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xvgr.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/compat/make_unique.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/gmxana/gstat.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/abstractdata.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/analysisdata.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/arraydata.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/dataframe.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/datamodule.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/average.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/displacement.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/histogram.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/lifetime.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/plot.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/nbsearch.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/indexutil.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/position.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selection.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectioncollection.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionenums.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoption.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoptionbehavior.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoptionmanager.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/analysismodule.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/analysissettings.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/topologyinformation.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs/usr/bin/gmx" to "$ORIGIN/../lib/arm-linux-gnueabihf" -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/bin -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx-completion.bash -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx-completion-gmx.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -j3 -C build/basic-dp install DESTDIR=/build/gromacs-2019.1/debian/gromacs make[1]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles /build/gromacs-2019.1/build/basic-dp/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= [ 4%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 5%] Built target tng_io_obj /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build [ 5%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 7%] Built target mdrun_objlib /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend [ 23%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= [ 24%] Built target view_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 24%] Built target mdrun_test_objlib make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 98%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/share/template /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/share/template /build/gromacs-2019.1/build/basic-dp/share/template/CMakeFiles/template.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'share/template/CMakeFiles/template.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [100%] Built target template [100%] Built target gmx make[2]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-view.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: 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Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-trajectory.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-saxs.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/spce.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.arn -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/atom_nom.tbl -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/flexspc.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/flexspce.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/dgsolv.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: 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Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ca-shift.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/CMakeLists.txt -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/README -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/template.cpp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/Makefile.pkg -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/cmake/FindGROMACS.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.bash -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.zsh -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.csh -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/bin/demux.pl -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/bin/xplor2gmx.pl -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/version.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs_d.so.4.0.0 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs_d.so.4 -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs_d.so.4.0.0" to "$ORIGIN/../lib/arm-linux-gnueabihf" -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs_d.so -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/pkgconfig/libgromacs_d.pc -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs_d/libgromacs.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs_d/libgromacs-release.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs_d/gromacs_d-config.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs_d/gromacs_d-config-version.cmake -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdlib/simulationsignal.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlinehelpwriter.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineinit.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlinemodule.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineoptionsmodule.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineparser.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineprogramcontext.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/filenm.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/pargs.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/viewit.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fft/fft.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/gpu_utils/hostallocator.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/linearalgebra/eigensolver.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/linearalgebra/matrix.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/linearalgebra/sparsematrix.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/3dtransforms.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/arrayrefwithpadding.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/do_fit.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/functions.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/gmxcomplex.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/units.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/utilities.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/vec.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/vectypes.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/paddedvector.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/inputrec.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/mdatom.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/md_enums.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/state.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/abstractoption.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/abstractsection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/basicoptions.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/filenameoption.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/filenameoptionmanager.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ioptionsbehavior.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ioptionscontainer.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ioptionscontainerwithsections.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/isectionstorage.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ivaluestore.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/optionfiletype.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/optionflags.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/options.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/optionsection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/repeatingsection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/timeunitmanager.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/valuestore.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/ishift.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/pbc.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/rmpbc.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/exponentialdistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/gammadistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/normaldistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/seed.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/tabulatednormaldistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/threefry.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/uniformintdistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/uniformrealdistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/restraint/restraintpotential.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/timing/wallcycle.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/timing/walltime_accounting.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/atomprop.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/atoms.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/block.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/forcefieldparameters.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/idef.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/ifunc.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/index.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/mtop_util.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/symtab.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/topology.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectory/energyframe.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectory/trajectoryframe.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/alignedallocator.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/allocator.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/arrayref.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/arraysize.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/basedefinitions.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/baseversion.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/classhelpers.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/cstringutil.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/current_function.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/datafilefinder.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/errorcodes.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/exceptions.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/fatalerror.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/flags.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/fileptr.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/futil.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/gmxassert.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/init.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/programcontext.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/real.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/smalloc.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/stringutil.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/unique_cptr.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/confio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/enxio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/filetypes.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/gmxfio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/matio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/mtxio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/oenv.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/pdbio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/rgb.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/tpxio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/trrio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/trxio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xdr_datatype.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xtcio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xvgr.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/compat/make_unique.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/gmxana/gstat.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/abstractdata.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/analysisdata.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/arraydata.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/dataframe.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/datamodule.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/average.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/displacement.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/histogram.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/lifetime.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/plot.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/nbsearch.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/indexutil.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/position.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectioncollection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionenums.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoption.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoptionbehavior.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoptionmanager.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/analysismodule.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/analysissettings.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/topologyinformation.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx_d -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs/usr/bin/gmx_d" to "$ORIGIN/../lib/arm-linux-gnueabihf" -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/bin -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx-completion.bash -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx-completion-gmx_d.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' dh_installman -pgromacs debian/man/demux.1 debian/man/xplor2gmx.1 # gmx(1) -> gmx_d(1) dh_link -pgromacs -pgromacs-data # temporary as of 2019-beta2 and removal of CMAKE_SKIP_RPATH chrpath -d /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx_d dh_testdir dh_testroot dh_prep -pgromacs-mpich dh_installdirs -pgromacs-mpich /usr/bin/make -j3 -C build/mpich install DESTDIR=/build/gromacs-2019.1/debian/gromacs-mpich make[1]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich/CMakeFiles /build/gromacs-2019.1/build/mpich/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 1%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend [ 3%] Built target tng_io_obj /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/programs /build/gromacs-2019.1/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 26%] Built target libgromacs_generated [ 26%] Built target mdrun_objlib [ 27%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/programs /build/gromacs-2019.1/build/mpich/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/mpich' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/mdrun_mpi.mpich -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/mdrun_mpi.mpich" to "$ORIGIN/../lib/arm-linux-gnueabihf" -- Installing: /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi.mpich.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -j3 -C build/mpich-dp install DESTDIR=/build/gromacs-2019.1/debian/gromacs-mpich make[1]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich-dp/CMakeFiles /build/gromacs-2019.1/build/mpich-dp/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 1%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend [ 3%] Built target tng_io_obj /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/programs /build/gromacs-2019.1/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 7%] Built target lmfit_objlib [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 27%] Built target mdrun_objlib make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/programs /build/gromacs-2019.1/build/mpich-dp/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/mdrun_mpi_d.mpich -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/mdrun_mpi_d.mpich" to "$ORIGIN/../lib/arm-linux-gnueabihf" -- Installing: /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi_d.mpich.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' chmod 644 /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/gmx-completion* mv /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi.mpich.bash /build/gromacs-2019.1/debian/gromacs-mpich/usr/share/bash-completion/completions/mdrun_mpi.mpich mv /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi_d.mpich.bash /build/gromacs-2019.1/debian/gromacs-mpich/usr/share/bash-completion/completions/mdrun_mpi_d.mpich # temporary as of 2019-beta2 chrpath -d /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/mdrun_mpi* dh_installman -pgromacs-mpich debian/man/mdrun_mpi.mpich.1 dh_link -pgromacs-mpich usr/share/man/man1/mdrun_mpi.mpich.1.gz usr/share/man/man1/mdrun_mpi_d.mpich.1.gz dh_lintian -pgromacs-mpich dh_testdir dh_testroot dh_prep -pgromacs-openmpi dh_installdirs -pgromacs-openmpi /usr/bin/make -j3 -C build/openmpi install DESTDIR=/build/gromacs-2019.1/debian/gromacs-openmpi make[1]: Entering directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/openmpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi/CMakeFiles /build/gromacs-2019.1/build/openmpi/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build [ 1%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 23%] Built target libgromacs_generated /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 26%] Built target tng_io_obj [ 27%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/programs /build/gromacs-2019.1/build/openmpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 27%] Built target mdrun_objlib make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/programs /build/gromacs-2019.1/build/openmpi/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/mdrun_mpi.openmpi -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/mdrun_mpi.openmpi" to "$ORIGIN/../lib/arm-linux-gnueabihf" -- Installing: /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi.openmpi.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -j3 -C build/openmpi-dp install DESTDIR=/build/gromacs-2019.1/debian/gromacs-openmpi make[1]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/openmpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 1%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 3%] Built target tng_io_obj /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/programs /build/gromacs-2019.1/build/openmpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 26%] Built target libgromacs_generated [ 26%] Built target mdrun_objlib [ 27%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/programs /build/gromacs-2019.1/build/openmpi-dp/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/mdrun_mpi_d.openmpi -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/mdrun_mpi_d.openmpi" to "$ORIGIN/../lib/arm-linux-gnueabihf" -- Installing: /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi_d.openmpi.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' chmod 644 /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/gmx-completion* mv /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi.openmpi.bash /build/gromacs-2019.1/debian/gromacs-openmpi/usr/share/bash-completion/completions/mdrun_mpi.openmpi mv /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi_d.openmpi.bash /build/gromacs-2019.1/debian/gromacs-openmpi/usr/share/bash-completion/completions/mdrun_mpi_d.openmpi # Force-disable RUNPATH - see # and lintian tag binary-or-shlib-defines-rpath in versions >= 2.5.50 chrpath -d /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/mdrun_mpi* dh_installman -pgromacs-openmpi debian/man/mdrun_mpi.openmpi.1 dh_link -pgromacs-openmpi usr/share/man/man1/mdrun_mpi.openmpi.1.gz usr/share/man/man1/mdrun_mpi_d.openmpi.1.gz dh_lintian -pgromacs-openmpi dh_testdir dh_testroot dh_prep -pgromacs-data -plibgromacs-dev dh_installdirs -pgromacs-data mv /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top \ /build/gromacs-2019.1/debian/gromacs-data/usr/share/gromacs mv /build/gromacs-2019.1/debian/gromacs/usr/share/man \ /build/gromacs-2019.1/debian/gromacs-data/usr/share/man # some of the default installation directories for documentation and # example shell scripts are not FHS-friendly; move them appropriately cat /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx*.bash > \ /build/gromacs-2019.1/debian/gromacs-data/usr/share/bash-completion/completions/gmx rm -f /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC* /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx*.bash # symlinks, primarily for /usr/share/doc/{gromacs,libgromacs*} -> gromacs-data dh_link -pgromacs-data # rename a pair of Perl scripts to drop the .pl extension (Policy 10.4) mv /build/gromacs-2019.1/debian/gromacs/usr/bin/demux.pl /build/gromacs-2019.1/debian/gromacs/usr/bin/demux mv /build/gromacs-2019.1/debian/gromacs/usr/bin/xplor2gmx.pl /build/gromacs-2019.1/debian/gromacs/usr/bin/xplor2gmx mkdir -p /build/gromacs-2019.1/debian/libgromacs4/usr/lib/arm-linux-gnueabihf mv /build/gromacs-2019.1/debian/gromacs/usr/lib/*/*.so.* /build/gromacs-2019.1/debian/libgromacs4/usr/lib/arm-linux-gnueabihf/ dh_installdirs -plibgromacs-dev mv /build/gromacs-2019.1/debian/gromacs/usr/include /build/gromacs-2019.1/debian/libgromacs-dev/usr/include # catch normal libraries plus all applicable MPI variants mkdir -p /build/gromacs-2019.1/debian/libgromacs-dev/usr/lib/arm-linux-gnueabihf mv /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/*.so \ /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf/pkgconfig \ /build/gromacs-2019.1/debian/libgromacs-dev/usr/lib/arm-linux-gnueabihf/ rmdir /build/gromacs-2019.1/debian/gromacs/usr/lib/arm-linux-gnueabihf /build/gromacs-2019.1/debian/gromacs/usr/lib mv /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template /build/gromacs-2019.1/debian/libgromacs-dev/usr/share/gromacs/template # remaining documentation catch-all mv /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/* /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs rmdir /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs # what are you doing here? mv /build/gromacs-2019.1/debian/gromacs/usr/share/cmake /build/gromacs-2019.1/debian/libgromacs-dev/usr/share/gromacs/ dh_lintian -pgromacs -pgromacs-data -plibgromacs4 dh_testdir dh_testroot dh_install -pgromacs-data rdfind -outputname /dev/null -makesymlinks true /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/ Now scanning "/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc", found 23772 files. Now have 23772 files in total. Removed 0 files due to nonunique device and inode. Total size is 187244690 bytes or 179 MiB Removed 5898 files due to unique sizes from list.17874 files left. Now eliminating candidates based on first bytes:removed 5251 files from list.12623 files left. Now eliminating candidates based on last bytes:removed 1350 files from list.11273 files left. Now eliminating candidates based on sha1 checksum:removed 1645 files from list.9628 files left. It seems like you have 9628 files that are not unique Totally, 16 MiB can be reduced. Now making results file /dev/null Now making symbolic links. creating Making 5601 links. symlinks -r -s -c /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/ dangling: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs-data/COPYING -> copyright absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_111.md5 -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_595.md5 changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_111.md5 -> ../html-full/inherit_graph_595.md5 absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000018_000049.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000018_000049.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000018_000049.xhtml -> ../html-lib/dir_000018_000049.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/lifetime_8h__incl.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/lifetime_8h__incl.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/lifetime_8h__incl.map -> ../html-full/lifetime_8h__incl.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arraydata_8h__incl.md5 -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/arraydata_8h__incl.md5 changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/arraydata_8h__incl.md5 -> ../html-full/arraydata_8h__incl.md5 absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/position_8h__incl.md5 -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/position_8h__incl.md5 changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/position_8h__incl.md5 -> ../html-full/position_8h__incl.md5 absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DoubleOptionInfo__coll__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1DoubleOptionInfo__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1DoubleOptionInfo__coll__graph.map -> ../html-full/classgmx_1_1DoubleOptionInfo__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/histogram_8h__incl.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/histogram_8h__incl.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/histogram_8h__incl.map -> ../html-full/histogram_8h__incl.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/seed_8h__incl.md5 -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/seed_8h__incl.md5 changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/seed_8h__incl.md5 -> ../html-full/seed_8h__incl.md5 absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_55.md5 -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_213.md5 changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_55.md5 -> ../html-full/inherit_graph_213.md5 absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000093_000015.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000093_000015.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000093_000015.xhtml -> ../html-lib/dir_000093_000015.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_27.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_96.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_27.svg -> ../html-full/inherit_graph_96.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__mdatoms-members.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__mdatoms-members.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__mdatoms-members.xhtml -> ../html-full/structt__mdatoms-members.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionmanager_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionoptionmanager_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionmanager_8h__incl.svg -> ../html-full/selectionoptionmanager_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_74.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_337.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_74.svg -> ../html-full/inherit_graph_337.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineinit_8h__dep__incl.md5 -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/cmdlineinit_8h__dep__incl.md5 changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlineinit_8h__dep__incl.md5 -> ../html-lib/cmdlineinit_8h__dep__incl.md5 absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_98.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_484.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_98.map -> ../html-full/inherit_graph_484.map absolute: 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-> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__inherit__graph.map -> classgmx_1_1SimulationInstabilityError__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineModuleManagerTestBase__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineModuleManagerTestBase__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineModuleManagerTestBase__inherit__graph.map -> classgmx_1_1test_1_1CommandLineModuleManagerTestBase__coll__graph.map absolute: 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/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__inherit__graph.map -> classgmx_1_1StandardInputStream__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineHelpModule__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineHelpModule__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineHelpModule__inherit__graph.map -> classgmx_1_1CommandLineHelpModule__coll__graph.map absolute: 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/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InvalidInputError__inherit__graph.map -> classgmx_1_1InvalidInputError__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisData__inherit__graph.map -> classgmx_1_1AnalysisData__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1Rdf__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1Rdf__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1Rdf__inherit__graph.map -> classgmx_1_1analysismodules_1_1anonymous__namespace_02rdf_8cpp_03_1_1Rdf__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02analysismodule_8cpp_03_1_1TrajectoryAnalysisModuleDataBasic__inherit__graph.map -> 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/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileNameOptionManager__inherit__graph.map -> classgmx_1_1FileNameOptionManager__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1internal_1_1BasicAverageHistogramModule__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1internal_1_1BasicAverageHistogramModule__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1internal_1_1BasicAverageHistogramModule__inherit__graph.map -> classgmx_1_1internal_1_1BasicAverageHistogramModule__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionStorage__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionStorage__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionStorage__inherit__graph.map -> classgmx_1_1Int64OptionStorage__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TrajectoryAnalysisModuleTestFixture__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TrajectoryAnalysisModuleTestFixture__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TrajectoryAnalysisModuleTestFixture__inherit__graph.map -> classgmx_1_1test_1_1TrajectoryAnalysisModuleTestFixture__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__context_01_4__inherit__graph.map -> structgmx_1_1OpenClTraits_3_01cl__context_01_4__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlineprogramcontext_8cpp_03_1_1DefaultExecutableEnvironment__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlineprogramcontext_8cpp_03_1_1DefaultExecutableEnvironment__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlineprogramcontext_8cpp_03_1_1DefaultExecutableEnvironment__inherit__graph.map -> classgmx_1_1anonymous__namespace_02cmdlineprogramcontext_8cpp_03_1_1DefaultExecutableEnvironment__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ConfMatch__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ConfMatch__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1ConfMatch__inherit__graph.map -> classgmx_1_1test_1_1ConfMatch__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1InconsistentInputError__inherit__graph.map -> classgmx_1_1InconsistentInputError__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataLifetimeModule__inherit__graph.map -> classgmx_1_1AnalysisDataLifetimeModule__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64Fast__inherit__graph.map -> classgmx_1_1ThreeFry2x64Fast__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classanonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOptionStorage__inherit__graph.map -> 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/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__inherit__graph.map -> structgmx_1_1OpenClTraits_3_01cl__program_01_4__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordsHelpTopic__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordsHelpTopic__coll__graph.map changed: 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/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FilteringExactTextMatch__inherit__graph.map -> classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsFilter__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsFilter__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsFilter__inherit__graph.map -> classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsFilter__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__inherit__graph.map -> classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1EnumOption__inherit__graph.map -> classgmx_1_1EnumOption__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__inherit__graph.map -> classgmx_1_1TextOutputFile__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileInputRedirector__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileInputRedirector__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileInputRedirector__inherit__graph.map -> classgmx_1_1test_1_1TestFileInputRedirector__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule__inherit__graph.map -> classgmx_1_1AnalysisDataSimpleHistogramModule__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataWeightedHistogramModule__inherit__graph.map -> 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classgmx_1_1CommandLineProgramContext__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Constraints_1_1CreationHelper__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Constraints_1_1CreationHelper__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Constraints_1_1CreationHelper__inherit__graph.map -> structgmx_1_1Constraints_1_1CreationHelper__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor__inherit__graph.map -> classgmx_1_1OptionsTypeVisitor__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTest__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTest__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTest__inherit__graph.map -> structgmx_1_1test_1_1HostAllocatorTest__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1Simd4Test__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1Simd4Test__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1Simd4Test__inherit__graph.map -> classgmx_1_1test_1_1Simd4Test__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockOptionsModule__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockOptionsModule__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockOptionsModule__inherit__graph.map -> classgmx_1_1test_1_1MockOptionsModule__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExceptionInfo__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExceptionInfo__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExceptionInfo__inherit__graph.map -> classgmx_1_1ExceptionInfo__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionOptionBehavior__inherit__graph.map -> classgmx_1_1SelectionOptionBehavior__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToVector__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToVector__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToVector__inherit__graph.map -> classgmx_1_1anonymous__namespace_02helpwritercontext_8cpp_03_1_1WrapperToVector__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOptionInfo__inherit__graph.map -> classgmx_1_1StringOptionInfo__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsListFormatter__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsListFormatter__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsListFormatter__inherit__graph.map -> classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsListFormatter__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classanonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOption__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classanonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOption__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classanonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOption__inherit__graph.map -> classanonymous__namespace_02abstractoptionstorage_8cpp_03_1_1MockOption__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionStorage__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionStorage__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionStorage__inherit__graph.map -> classgmx_1_1IntegerOptionStorage__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1CommandsHelpTopic__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1CommandsHelpTopic__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1CommandsHelpTopic__inherit__graph.map -> classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1CommandsHelpTopic__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOptionInfo__inherit__graph.map -> classgmx_1_1IntegerOptionInfo__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1ModuleHelpTopic__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1ModuleHelpTopic__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1ModuleHelpTopic__inherit__graph.map -> classgmx_1_1anonymous__namespace_02cmdlinehelpmodule_8cpp_03_1_1ModuleHelpTopic__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1Int64OptionInfo__inherit__graph.map -> classgmx_1_1Int64OptionInfo__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1IntegerOption__inherit__graph.map -> classgmx_1_1IntegerOption__coll__graph.map dh_testdir dh_testroot dh_installchangelogs -i dh_installdocs -pgromacs-data dh_compress -i -X.pdf dh_fixperms -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'gromacs-data' in '../gromacs-data_2019.1-1_all.deb'. dh_testdir -a dh_testroot -a dh_installchangelogs -a dh_installdocs -a dh_strip -A dh_compress -a dh_fixperms -a dh_makeshlibs -a dh_shlibdeps -plibgromacs4 -L libgromacs4 -l debian/libgromacs4/usr/lib dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libgromacs4/usr/lib/arm-linux-gnueabihf/libgromacs.so.4.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libgromacs4/usr/lib/arm-linux-gnueabihf/libgromacs_d.so.4.0.0 found in none of the libraries dh_shlibdeps -pgromacs -L libgromacs4 -l debian/libgromacs4/usr/lib:debian/gromacs/usr/lib dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l debian/gromacs-mpich/usr/lib dpkg-shlibdeps: warning: debian/gromacs-mpich/usr/bin/mdrun_mpi_d.mpich contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/gromacs-mpich/usr/bin/mdrun_mpi.mpich contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib dpkg-shlibdeps: warning: debian/gromacs-openmpi/usr/bin/mdrun_mpi_d.openmpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/gromacs-openmpi/usr/bin/mdrun_mpi.openmpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libgromacs-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_installdeb -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'gromacs-mpich-dbgsym' in '../gromacs-mpich-dbgsym_2019.1-1_armhf.deb'. dpkg-deb: building package 'gromacs' in '../gromacs_2019.1-1_armhf.deb'. dpkg-deb: building package 'libgromacs4-dbgsym' in '../libgromacs4-dbgsym_2019.1-1_armhf.deb'. dpkg-deb: building package 'gromacs-dbgsym' in '../gromacs-dbgsym_2019.1-1_armhf.deb'. dpkg-deb: building package 'libgromacs4' in '../libgromacs4_2019.1-1_armhf.deb'. dpkg-deb: building package 'gromacs-openmpi' in '../gromacs-openmpi_2019.1-1_armhf.deb'. dpkg-deb: building package 'libgromacs-dev' in '../libgromacs-dev_2019.1-1_armhf.deb'. dpkg-deb: building package 'gromacs-mpich' in '../gromacs-mpich_2019.1-1_armhf.deb'. dpkg-deb: building package 'gromacs-openmpi-dbgsym' in '../gromacs-openmpi-dbgsym_2019.1-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gromacs_2019.1-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/13803 and its subdirectories I: Current time: Wed Sep 23 11:32:07 -12 2020 I: pbuilder-time-stamp: 1600903927